HEADER TRANSFERASE 06-JAN-06 2FM4 TITLE NMR STRUCTURE OF THE PHOSPHORYL CARRIER DOMAIN OF PYRUVATE PHOSPHATE TITLE 2 DIKINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE, PHOSPHATE DIKINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRUVATE, ORTHOPHOSPHATE DIKINASE; COMPND 5 EC: 2.7.9.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM SYMBIOSUM; SOURCE 3 ORGANISM_TAXID: 1512; SOURCE 4 GENE: PPDK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOHISTIDINE CARRIER DOMAIN, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR J.B.AMES REVDAT 4 29-MAY-24 2FM4 1 REMARK REVDAT 3 09-MAR-22 2FM4 1 REMARK REVDAT 2 24-FEB-09 2FM4 1 VERSN REVDAT 1 03-OCT-06 2FM4 0 JRNL AUTH Y.LIN,J.D.LUSIN,D.YE,D.DUNAWAY-MARIANO,J.B.AMES JRNL TITL EXAMINATION OF THE STRUCTURE, STABILITY, AND CATALYTIC JRNL TITL 2 POTENTIAL IN THE ENGINEERED PHOSPHORYL CARRIER DOMAIN OF JRNL TITL 3 PYRUVATE PHOSPHATE DIKINASE. JRNL REF BIOCHEMISTRY V. 45 1702 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16460017 JRNL DOI 10.1021/BI051816L REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.0, X-PLOR 3.0 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FM4 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000036041. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.07 M REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM CENT-I U-15N,13C; 20 MM REMARK 210 PHOSPHATE BUFFER, PH 7.0, 95% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 4D_13C REMARK 210 -SEPARATED_NOESY; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD 3D REMARK 210 HETERONUCLEAR NMR REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 H SER A 501 H THR A 502 1.25 REMARK 500 OD1 ASP A 494 H TYR A 495 1.47 REMARK 500 O ARG A 449 HG SER A 469 1.49 REMARK 500 O ALA A 457 H ARG A 461 1.55 REMARK 500 O PRO A 433 H ILE A 436 1.56 REMARK 500 O ALA A 491 H GLY A 493 1.57 REMARK 500 O GLY A 389 H VAL A 391 1.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 HIS A 418 CG HIS A 418 ND1 -0.120 REMARK 500 1 HIS A 440 CG HIS A 440 ND1 -0.120 REMARK 500 1 HIS A 455 CG HIS A 455 ND1 -0.120 REMARK 500 1 HIS A 488 CG HIS A 488 ND1 -0.141 REMARK 500 2 HIS A 418 CG HIS A 418 ND1 -0.121 REMARK 500 2 HIS A 440 CG HIS A 440 ND1 -0.122 REMARK 500 2 HIS A 455 CG HIS A 455 ND1 -0.119 REMARK 500 2 HIS A 488 CG HIS A 488 ND1 -0.144 REMARK 500 3 HIS A 418 CG HIS A 418 ND1 -0.124 REMARK 500 3 HIS A 440 CG HIS A 440 ND1 -0.121 REMARK 500 3 HIS A 455 CG HIS A 455 ND1 -0.120 REMARK 500 3 HIS A 488 CG HIS A 488 ND1 -0.144 REMARK 500 4 HIS A 418 CG HIS A 418 ND1 -0.119 REMARK 500 4 HIS A 440 CG HIS A 440 ND1 -0.121 REMARK 500 4 HIS A 455 CG HIS A 455 ND1 -0.121 REMARK 500 4 HIS A 488 CG HIS A 488 ND1 -0.142 REMARK 500 5 HIS A 418 CG HIS A 418 ND1 -0.121 REMARK 500 5 HIS A 440 CG HIS A 440 ND1 -0.120 REMARK 500 5 HIS A 455 CG HIS A 455 ND1 -0.122 REMARK 500 5 HIS A 488 CG HIS A 488 ND1 -0.144 REMARK 500 6 HIS A 418 CG HIS A 418 ND1 -0.121 REMARK 500 6 HIS A 440 CG HIS A 440 ND1 -0.121 REMARK 500 6 HIS A 455 CG HIS A 455 ND1 -0.121 REMARK 500 6 HIS A 488 CG HIS A 488 ND1 -0.147 REMARK 500 7 HIS A 418 CG HIS A 418 ND1 -0.123 REMARK 500 7 HIS A 440 CG HIS A 440 ND1 -0.120 REMARK 500 7 HIS A 455 CG HIS A 455 ND1 -0.121 REMARK 500 7 HIS A 488 CG HIS A 488 ND1 -0.140 REMARK 500 8 HIS A 418 CG HIS A 418 ND1 -0.120 REMARK 500 8 HIS A 440 CG HIS A 440 ND1 -0.119 REMARK 500 8 HIS A 455 CG HIS A 455 ND1 -0.120 REMARK 500 8 HIS A 488 CG HIS A 488 ND1 -0.142 REMARK 500 9 HIS A 418 CG HIS A 418 ND1 -0.120 REMARK 500 9 HIS A 440 CG HIS A 440 ND1 -0.121 REMARK 500 9 HIS A 455 CG HIS A 455 ND1 -0.119 REMARK 500 9 HIS A 488 CG HIS A 488 ND1 -0.139 REMARK 500 10 HIS A 418 CG HIS A 418 ND1 -0.122 REMARK 500 10 HIS A 440 CG HIS A 440 ND1 -0.120 REMARK 500 10 HIS A 455 CG HIS A 455 ND1 -0.121 REMARK 500 10 HIS A 488 CG HIS A 488 ND1 -0.143 REMARK 500 11 HIS A 418 CG HIS A 418 ND1 -0.119 REMARK 500 11 HIS A 440 CG HIS A 440 ND1 -0.123 REMARK 500 11 HIS A 455 CG HIS A 455 ND1 -0.121 REMARK 500 11 HIS A 488 CG HIS A 488 ND1 -0.141 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ALA A 385 -159.50 52.15 REMARK 500 1 LEU A 386 12.09 50.37 REMARK 500 1 ALA A 388 23.94 -171.97 REMARK 500 1 GLU A 390 36.88 -68.12 REMARK 500 1 SER A 394 108.47 -164.51 REMARK 500 1 ALA A 395 -146.42 -84.84 REMARK 500 1 PRO A 397 93.07 -69.92 REMARK 500 1 PRO A 400 100.83 -54.31 REMARK 500 1 TYR A 408 139.90 -170.98 REMARK 500 1 GLU A 422 -145.89 64.24 REMARK 500 1 GLU A 430 139.76 -176.40 REMARK 500 1 GLU A 434 -30.93 -35.23 REMARK 500 1 GLU A 443 3.83 -56.18 REMARK 500 1 ARG A 449 -136.04 -99.54 REMARK 500 1 SER A 454 -178.29 -174.29 REMARK 500 1 CYS A 471 -159.39 -100.69 REMARK 500 1 ILE A 474 110.28 -39.09 REMARK 500 1 ALA A 480 -103.67 -171.68 REMARK 500 1 LYS A 481 65.87 -155.96 REMARK 500 1 GLU A 492 69.49 -67.29 REMARK 500 1 SER A 501 1.55 174.31 REMARK 500 1 THR A 502 -21.03 -168.66 REMARK 500 2 ALA A 388 22.53 -164.26 REMARK 500 2 ALA A 395 -152.80 -142.46 REMARK 500 2 ALA A 398 -76.03 -59.89 REMARK 500 2 PRO A 400 104.04 -57.08 REMARK 500 2 GLU A 422 165.65 62.38 REMARK 500 2 ARG A 423 80.33 45.00 REMARK 500 2 GLU A 443 21.34 -59.95 REMARK 500 2 ARG A 449 -142.22 -121.13 REMARK 500 2 THR A 453 87.92 42.43 REMARK 500 2 SER A 454 -164.64 -160.06 REMARK 500 2 GLU A 473 66.67 -155.67 REMARK 500 2 GLU A 479 -7.43 -52.92 REMARK 500 2 ALA A 480 -82.30 -179.72 REMARK 500 2 LYS A 481 89.18 169.17 REMARK 500 2 ALA A 491 -124.31 -152.10 REMARK 500 2 GLU A 492 49.03 -67.90 REMARK 500 2 SER A 501 4.47 171.15 REMARK 500 2 THR A 502 -22.79 -168.38 REMARK 500 2 ASP A 509 108.97 -42.19 REMARK 500 3 GLU A 390 59.04 -92.37 REMARK 500 3 VAL A 391 156.06 -46.30 REMARK 500 3 SER A 394 122.18 177.12 REMARK 500 3 ALA A 395 -151.69 -114.36 REMARK 500 3 PRO A 397 97.32 -63.08 REMARK 500 3 PRO A 400 98.06 -54.91 REMARK 500 3 GLU A 422 148.60 65.96 REMARK 500 3 ARG A 423 95.01 55.89 REMARK 500 3 GLU A 430 -165.53 -109.30 REMARK 500 REMARK 500 THIS ENTRY HAS 259 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 423 0.13 SIDE CHAIN REMARK 500 1 ARG A 428 0.30 SIDE CHAIN REMARK 500 1 ARG A 449 0.16 SIDE CHAIN REMARK 500 1 ARG A 461 0.25 SIDE CHAIN REMARK 500 2 ARG A 423 0.30 SIDE CHAIN REMARK 500 2 ARG A 428 0.16 SIDE CHAIN REMARK 500 2 ARG A 449 0.24 SIDE CHAIN REMARK 500 2 ARG A 461 0.31 SIDE CHAIN REMARK 500 3 ARG A 423 0.31 SIDE CHAIN REMARK 500 3 ARG A 428 0.25 SIDE CHAIN REMARK 500 3 ARG A 449 0.20 SIDE CHAIN REMARK 500 3 ARG A 461 0.21 SIDE CHAIN REMARK 500 4 ARG A 423 0.14 SIDE CHAIN REMARK 500 4 ARG A 428 0.29 SIDE CHAIN REMARK 500 4 ARG A 449 0.12 SIDE CHAIN REMARK 500 4 ARG A 461 0.11 SIDE CHAIN REMARK 500 5 ARG A 423 0.24 SIDE CHAIN REMARK 500 5 ARG A 428 0.25 SIDE CHAIN REMARK 500 5 ARG A 449 0.25 SIDE CHAIN REMARK 500 5 ARG A 461 0.23 SIDE CHAIN REMARK 500 6 ARG A 423 0.32 SIDE CHAIN REMARK 500 6 ARG A 428 0.23 SIDE CHAIN REMARK 500 6 ARG A 449 0.17 SIDE CHAIN REMARK 500 6 ARG A 461 0.12 SIDE CHAIN REMARK 500 7 ARG A 423 0.28 SIDE CHAIN REMARK 500 7 ARG A 428 0.32 SIDE CHAIN REMARK 500 7 ARG A 461 0.26 SIDE CHAIN REMARK 500 8 ARG A 423 0.24 SIDE CHAIN REMARK 500 8 ARG A 428 0.25 SIDE CHAIN REMARK 500 8 ARG A 449 0.32 SIDE CHAIN REMARK 500 8 ARG A 461 0.32 SIDE CHAIN REMARK 500 9 ARG A 423 0.14 SIDE CHAIN REMARK 500 9 ARG A 428 0.31 SIDE CHAIN REMARK 500 9 ARG A 449 0.32 SIDE CHAIN REMARK 500 9 ARG A 461 0.25 SIDE CHAIN REMARK 500 10 ARG A 423 0.09 SIDE CHAIN REMARK 500 10 ARG A 428 0.28 SIDE CHAIN REMARK 500 10 ARG A 449 0.32 SIDE CHAIN REMARK 500 10 ARG A 461 0.29 SIDE CHAIN REMARK 500 11 ARG A 423 0.32 SIDE CHAIN REMARK 500 11 ARG A 428 0.32 SIDE CHAIN REMARK 500 11 ARG A 449 0.28 SIDE CHAIN REMARK 500 11 ARG A 461 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2FM4 A 384 511 UNP P22983 PPDK_CLOSY 383 510 SEQRES 1 A 128 ALA ALA LEU LYS ALA GLY GLU VAL ILE GLY SER ALA LEU SEQRES 2 A 128 PRO ALA SER PRO GLY ALA ALA ALA GLY LYS VAL TYR PHE SEQRES 3 A 128 THR ALA ASP GLU ALA LYS ALA ALA HIS GLU LYS GLY GLU SEQRES 4 A 128 ARG VAL ILE LEU VAL ARG LEU GLU THR SER PRO GLU ASP SEQRES 5 A 128 ILE GLU GLY MET HIS ALA ALA GLU GLY ILE LEU THR VAL SEQRES 6 A 128 ARG GLY GLY MET THR SER HIS ALA ALA VAL VAL ALA ARG SEQRES 7 A 128 GLY MET GLY THR CYS CYS VAL SER GLY CYS GLY GLU ILE SEQRES 8 A 128 LYS ILE ASN GLU GLU ALA LYS THR PHE GLU LEU GLY GLY SEQRES 9 A 128 HIS THR PHE ALA GLU GLY ASP TYR ILE SER LEU ASP GLY SEQRES 10 A 128 SER THR GLY LYS ILE TYR LYS GLY ASP ILE GLU HELIX 1 1 THR A 410 GLY A 421 1 12 HELIX 2 2 ASP A 435 ALA A 442 1 8 HELIX 3 3 SER A 454 GLY A 464 1 11 SHEET 1 A 4 LEU A 396 SER A 399 0 SHEET 2 A 4 CYS A 466 SER A 469 -1 O SER A 469 N LEU A 396 SHEET 3 A 4 GLY A 444 LEU A 446 1 N ILE A 445 O VAL A 468 SHEET 4 A 4 ILE A 425 LEU A 426 1 N LEU A 426 O LEU A 446 SHEET 1 B 3 GLY A 401 LYS A 406 0 SHEET 2 B 3 TYR A 495 GLY A 500 -1 O LEU A 498 N ALA A 403 SHEET 3 B 3 ILE A 505 LYS A 507 -1 O TYR A 506 N SER A 497 SHEET 1 C 2 PHE A 483 LEU A 485 0 SHEET 2 C 2 HIS A 488 PHE A 490 -1 O HIS A 488 N LEU A 485 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11