6PTR

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Bartonella birtlesii bound to griselimycin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of a DnaN sliding clamp (DNA polymerase III subunit beta) from Bartonella birtlesii bound to griselimycin

Edwards, T.E., Abendroth, J., Horanyi, P.S., Lorimer, D.D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta sliding clampA,
C [auth B]		381Bartonella birtlesii LL-WM9Mutation(s): 0 
Gene Names: ME7_01154
UniProt
Find proteins for J1IY24 (Bartonella birtlesii LL-WM9)
Explore J1IY24 
Go to UniProtKB:  J1IY24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupJ1IY24
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLYB [auth X],
D [auth Y]		11Streptomyces griseusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD
Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
R [auth B],
S [auth B],
T [auth B],
U [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
EDO
Query on EDO
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
MP8
Query on MP8		B [auth X],
D [auth Y]		L-PEPTIDE LINKINGC6 H11 N O2PRO
MVA
Query on MVA		B [auth X],
D [auth Y]		L-PEPTIDE LINKINGC6 H13 N O2VAL
NZC
Query on NZC		B [auth X],
D [auth Y]		L-PEPTIDE LINKINGC5 H11 N O3THR
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.95α = 90
b = 93.13β = 90
c = 110.74γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2023-11-15
    Changes: Data collection, Derived calculations