3DV8 | pdb_00003dv8

Crystal structure of a putative transcriptional regulator of the crp/fnr family (eubrec_1222) from eubacterium rectale atcc 33656 at 2.55 A resolution

PDB DOI: https://doi.org/10.2210/pdb3DV8/pdb

Classification: TRANSCRIPTION
Organism(s): Agathobacter rectalis ATCC 33656
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-07-18 Released: 2008-08-05
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free:
0.262 (Depositor), 0.277 (DCC)
R-Value Work:
0.222 (Depositor), 0.228 (DCC)
R-Value Observed:
0.224 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3DV8

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of transcriptional regulator, Crp/Fnr family (RER070207001219) from Eubacterium rectale at 2.55 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 25.86 kDa
Atom Count: 1,810
Modeled Residue Count: 216
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcriptional regulator, Crp/Fnr family	A	220	Agathobacter rectalis ATCC 33656	Mutation(s): 0 Gene Names: RER070207001219
UniProt
Find proteins for A5ZWV4 (Blautia obeum ATCC 29174) Explore A5ZWV4 Go to UniProtKB: A5ZWV4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A5ZWV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.55 Å
R-Value Free: 0.262 (Depositor), 0.277 (DCC)
R-Value Work: 0.222 (Depositor), 0.228 (DCC)
R-Value Observed: 0.224 (Depositor)

Diffraction Data:

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.56	α = 90
b = 88.482	β = 90
c = 181.304	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-08-05

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Structure summary

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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.