3GKU | pdb_00003gku

Crystal structure of a probable RNA-binding protein from Clostridium symbiosum ATCC 14940

PDB DOI: https://doi.org/10.2210/pdb3GKU/pdb

Classification: RNA BINDING PROTEIN
Organism(s): [Clostridium] symbiosum ATCC 14940
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-11 Released: 2009-03-31
Deposition Author(s): Tan, K., Keigher, L., Jedrzejczak, R., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.287 (Depositor), 0.283 (DCC)
R-Value Work:
0.220 (Depositor), 0.219 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of a probable RNA-binding protein from Clostridium symbiosum ATCC 14940

Tan, K., Keigher, L., Jedrzejczak, R., Babnigg, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 78.58 kDa
Atom Count: 4,131
Modeled Residue Count: 533
Deposited Residue Count: 675
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable RNA-binding protein	A, B, C	225	[Clostridium] symbiosum ATCC 14940	Mutation(s): 0
UniProt
Find proteins for D0VX24 (Clostridium symbiosum) Explore D0VX24 Go to UniProtKB: D0VX24
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0VX24
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.287 (Depositor), 0.283 (DCC)
R-Value Work: 0.220 (Depositor), 0.219 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.992	α = 90
b = 126.992	β = 90
c = 106.185	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-03-31

Deposition Author(s):

Jedrzejczak, R.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

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.