3EUS | pdb_00003eus

The crystal structure of the DNA binding protein from Silicibacter pomeroyi

PDB DOI: https://doi.org/10.2210/pdb3EUS/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Ruegeria pomeroyi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-10-10 Released: 2008-11-25
Deposition Author(s): Zhang, R., Li, H., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.254 (Depositor), 0.288 (DCC)
R-Value Work:
0.201 (Depositor), 0.239 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of the DNA binding protein from Silicibacter pomeroyi

Zhang, R., Li, H., Freeman, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 19.4 kDa
Atom Count: 1,376
Modeled Residue Count: 162
Deposited Residue Count: 172
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein	A, B	86	Ruegeria pomeroyi	Mutation(s): 0 Gene Names: GI:56696110, SPO1217
UniProt
Find proteins for Q5LU41 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LU41 Go to UniProtKB: Q5LU41
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LU41
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.254 (Depositor), 0.288 (DCC)
R-Value Work: 0.201 (Depositor), 0.239 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.164	α = 90
b = 60.641	β = 90
c = 68.506	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-11-25

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-11-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2023-12-27
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.