5X06

DNA replication regulation protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Replication regulation protein

Kim, J.Cho, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit beta
A, B, C, D
386Escherichia coli O157:H7Mutation(s): 0 
Gene Names: dnaNZ5192ECs4636
EC: 2.7.7.7
UniProt
Find proteins for P0A988 (Escherichia coli (strain K12))
Explore P0A988 
Go to UniProtKB:  P0A988
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A988
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DnaA regulatory inactivator Hda
E, F, G, H
253Escherichia coli O157:H7Mutation(s): 0 
Gene Names: hdaZ3759ECs3358
UniProt
Find proteins for P69931 (Escherichia coli (strain K12))
Explore P69931 
Go to UniProtKB:  P69931
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69931
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
K [auth E],
N [auth F],
P [auth G],
S [auth H]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth C],
J [auth D],
M [auth E],
R [auth G]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth E],
O [auth F],
Q [auth G],
T [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.112α = 90
b = 149.542β = 90
c = 200.78γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation of Korea funded by the Korea GovernmentKorea, Republic OfNRF-2015R1A2A1A05001694
National Research Foundation of Korea funded by the Korea GovernmentKorea, Republic Of2012054226
National Research Foundation of Korea funded by the Korea GovernmentKorea, Republic Of20120008833

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description