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

Validation slider image for 3GKU

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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View more in-depth experimental data

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

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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.