HEADER HYDROLASE 14-MAY-20 7C3Z TITLE THE STRUCTURE OF CLASS II TUMOR SUPPRESSOR PROTEIN H-REV107 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HRAS-LIKE SUPPRESSOR 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOLIPASE A AND ACYLTRANSFERASE 3,ADIPOSE-SPECIFIC COMPND 5 PHOSPHOLIPASE A2,ADPLA,GROUP XVI PHOSPHOLIPASE A1/A2,H-REV 107 COMPND 6 PROTEIN HOMOLOG,HREV107-1,HRAS-LIKE SUPPRESSOR 1,HRSL3,HREV107-3, COMPND 7 RENAL CARCINOMA ANTIGEN NY-REN-65; COMPND 8 EC: 3.1.1.32,3.1.1.4; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PLAAT3, HRASLS3, HREV107, PLA2G16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS H-REV107, HREV107 TYPE II TUMOR SUPPRESSOR GENE, RETINOID-INDUCIBLE KEYWDS 2 GENE 1, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.W.HAN,M.S.JEONG,S.B.JANG REVDAT 2 29-NOV-23 7C3Z 1 REMARK REVDAT 1 19-MAY-21 7C3Z 0 JRNL AUTH C.W.HAN,M.S.JEONG,S.C.HA,S.B.JANG JRNL TITL A H-REV107 PEPTIDE INHIBITS TUMOR GROWTH AND INTERACTS JRNL TITL 2 DIRECTLY WITH ONCOGENIC KRAS MUTANTS. JRNL REF CANCERS (BASEL) V. 12 2020 JRNL REFN ESSN 2072-6694 JRNL PMID 32486141 JRNL DOI 10.3390/CANCERS12061412 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 10763 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 546 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.4610 - 3.1051 1.00 2670 144 0.2402 0.2444 REMARK 3 2 3.1051 - 2.4650 1.00 2563 134 0.2443 0.2757 REMARK 3 3 2.4650 - 2.1535 1.00 2519 136 0.2201 0.2981 REMARK 3 4 2.1535 - 1.9570 0.99 2465 132 0.2058 0.2772 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 862 REMARK 3 ANGLE : 0.889 1171 REMARK 3 CHIRALITY : 0.051 124 REMARK 3 PLANARITY : 0.006 152 REMARK 3 DIHEDRAL : 3.840 517 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7C3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1300016960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10814 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4DOT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POLYETHYLENE GLYCOL 3,350 AND 0.2 M REMARK 280 POTASSIUM NITRATE AT PH 6.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 21.46750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.39800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.49800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.39800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.46750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.49800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 40 REMARK 465 GLU A 41 REMARK 465 VAL A 42 REMARK 465 ALA A 43 REMARK 465 GLY A 44 REMARK 465 ALA A 45 REMARK 465 GLY A 46 REMARK 465 ALA A 47 REMARK 465 ALA A 48 REMARK 465 SER A 49 REMARK 465 VAL A 50 REMARK 465 MET A 51 REMARK 465 SER A 52 REMARK 465 ALA A 53 REMARK 465 LEU A 54 REMARK 465 THR A 55 REMARK 465 ASP A 56 REMARK 465 LYS A 57 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 N ALA A 58 O HOH A 201 2.02 REMARK 500 SG CYS A 89 O HOH A 251 2.09 REMARK 500 O HOH A 255 O HOH A 256 2.14 REMARK 500 OG SER A 71 O HOH A 202 2.18 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 LEU A 105 30.24 -92.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 256 DISTANCE = 6.84 ANGSTROMS DBREF 7C3Z A 5 125 UNP P53816 PLAT3_HUMAN 5 125 SEQADV 7C3Z HIS A 126 UNP P53816 EXPRESSION TAG SEQADV 7C3Z HIS A 127 UNP P53816 EXPRESSION TAG SEQADV 7C3Z HIS A 128 UNP P53816 EXPRESSION TAG SEQADV 7C3Z HIS A 129 UNP P53816 EXPRESSION TAG SEQADV 7C3Z HIS A 130 UNP P53816 EXPRESSION TAG SEQADV 7C3Z HIS A 131 UNP P53816 EXPRESSION TAG SEQRES 1 A 127 ILE PRO GLU PRO LYS PRO GLY ASP LEU ILE GLU ILE PHE SEQRES 2 A 127 ARG PRO PHE TYR ARG HIS TRP ALA ILE TYR VAL GLY ASP SEQRES 3 A 127 GLY TYR VAL VAL HIS LEU ALA PRO PRO SER GLU VAL ALA SEQRES 4 A 127 GLY ALA GLY ALA ALA SER VAL MET SER ALA LEU THR ASP SEQRES 5 A 127 LYS ALA ILE VAL LYS LYS GLU LEU LEU TYR ASP VAL ALA SEQRES 6 A 127 GLY SER ASP LYS TYR GLN VAL ASN ASN LYS HIS ASP ASP SEQRES 7 A 127 LYS TYR SER PRO LEU PRO CYS SER LYS ILE ILE GLN ARG SEQRES 8 A 127 ALA GLU GLU LEU VAL GLY GLN GLU VAL LEU TYR LYS LEU SEQRES 9 A 127 THR SER GLU ASN CYS GLU HIS PHE VAL ASN GLU LEU ARG SEQRES 10 A 127 TYR GLY VAL ALA HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *56(H2 O) HELIX 1 AA1 LEU A 65 GLY A 70 1 6 HELIX 2 AA2 PRO A 88 VAL A 100 1 13 HELIX 3 AA3 THR A 109 GLY A 123 1 15 SHEET 1 AA1 5 ILE A 59 LEU A 64 0 SHEET 2 AA1 5 TYR A 32 ALA A 37 -1 N HIS A 35 O LYS A 61 SHEET 3 AA1 5 TYR A 21 GLY A 29 -1 N VAL A 28 O TYR A 32 SHEET 4 AA1 5 LEU A 13 ARG A 18 -1 N ILE A 16 O HIS A 23 SHEET 5 AA1 5 LYS A 73 VAL A 76 -1 O LYS A 73 N PHE A 17 CRYST1 42.935 52.996 62.796 90.00 90.00 90.00 P 21 21 21 4 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 0.023291 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018869 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015925 0.00000