› 3wvp

X-ray diffraction
2.3Å resolution

Time-Resolved Crystal Structure of HindIII with 60sec soaking

Released:
DOI: 10.2210/pdb3wvp/pdb
PDB entry 3wvp coloured by chain, front view.
PDB entry 3wvp coloured by chain, side view.
PDB entry 3wvp coloured by chain, top view.
Source organisms:
Primary publication:
Analysis of the HindIII-catalyzed reaction by time-resolved crystallography.
Kawamura T, Kobayashi T, Watanabe N
OpenAccess logo Acta Crystallogr D Biol Crystallogr 71 256-65 (2015)
PMID: 25664735

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetramer
hetero hexamer (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-218954 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
Type II restriction enzyme HindIII Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 300 amino acids
Theoretical weight: 35 KDa
Source organism: Haemophilus influenzae Rd KW20
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P43870 (Residues: 1-300; Coverage: 100%)
Gene names: HI_1393, hindIIIR
Sequence domains: HindIII restriction endonuclease
Structure domains:
DNA (5'-D(*GP*CP*CP*AP*AP*GP*CP*TP*TP*GP*GP*C)-3') Chains: E, F, G, H, I, J, K, L
Molecule details ›
Chains: E, F, G, H, I, J, K, L
Length: 12 nucleotides
Theoretical weight: 3.66 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*AP*GP*CP*TP*TP*GP*GP*C)-3') Chains: M, N, Q, R
Molecule details ›
Chains: M, N, Q, R
Length: 8 nucleotides
Theoretical weight: 2.44 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*CP*A)-3') Chains: O, P, S, T
Molecule details ›
Chains: O, P, S, T
Length: 4 nucleotides
Theoretical weight: 1.18 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand GOL 4 x GOL
Ligand MN 8 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 80.495Å b: 140.704Å c: 96.467Å
α: 90° β: 112.07° γ: 90°
R-values:
R R work R free
0.184 0.182 0.23
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 mention without citation

Analysis of the HindIII-catalyzed reaction by time-resolved crystallography.
Kawamura et al. (2015)