4YFU

Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history. 



Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymeraseA,
B [auth D]		580Geobacillus stearothermophilusMutation(s): 2 
EC: 2.7.7.7
UniProt
Find proteins for E1C9K5 (Geobacillus stearothermophilus)
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Go to UniProtKB:  E1C9K5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K5
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
Primer DNAC [auth B],
E		9synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
Template DNAD [auth C],
F		14synthetic construct
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
G, H
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP
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I [auth A]THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
J [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME		A,
B [auth D]		L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.23α = 90
b = 108.1β = 90
c = 151.34γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Released Date: 2015-07-22 
    • Deposition Author(s): Wu, E.Y.
Funding OrganizationLocationGrant Number
Jeffress TrustUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Refinement description
  • Version 1.2: 2015-09-16
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2022-04-13
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary