3DV8

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
R-Value Work: 0.222
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

This is version 1.3 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
Modelled Residue Count: 216
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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
R-Value Work: 0.222
R-Value Observed: 0.224
Space Group: I 2 2 2
Diffraction Data: https://doi.org/10.18430/M33DV8

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

View Full Validation Report

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.