3HPO

Crystal structure of fragment DNA polymerase I from Bacillus stearothermophilus Y714S mutant bound to G:T mismatch

Structural Biology Knowledgebase: 3HPO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 3HPO

Classification: TRANSFERASE / DNA

Total Structure Weight: 72860.24


Macromolecule Entities
Molecule Chains Length Organism Details
DNA polymerase I, large fragment A 580 Geobacillus stearothermophilus EC#: 2.7.7.7 IUBMB
Fragment: Residues 297-876
Mutation: D329A, Y714S
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*CP*GP*AP*TP*CP*AP*CP*GP*(DOC))-3' B 9 synthetic
5'-D(P*GP*GP*CP*GP*TP*GP*AP*TP*CP*G)-3' C 10 synthetic

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TTP
Query on TTP

A THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

A SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
CME
Query on CME
A L-PEPTIDE LINKING C5 H11 N O3 S2 CYS
DOC
Query on DOC
B DNA LINKING C9 H14 N3 O6 P DC

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.201
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 90.21 α = 90.00
b = 93.73 β = 90.00
c = 105.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-06-04
  • Released Date: 2010-06-23
  • Deposition author(s): Wu, E.Y., Beese, L.S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4