5TBF | pdb_00005tbf

Crystal structure of SeMet derivatives of domain2 and domain 3 of RctB

PDB DOI: https://doi.org/10.2210/pdb5TBF/pdb

Classification: TRANSLATION
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-09-12 Released: 2017-04-12
Deposition Author(s): Li, M., Wlodawer, A., Chattoraj, D., Jha, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.278 (Depositor), 0.239 (DCC)
R-Value Work:
0.220 (Depositor), 0.224 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5TBF

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of core domains of RctB

Li, M., Wlodawer, A., Jha, J., Chattoraj, D., Gustchina, A.

To be published.

Macromolecule Content

Total Structure Weight: 76.94 kDa
Atom Count: 4,558
Modeled Residue Count: 553
Deposited Residue Count: 652
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation elongation factor	A, B	326	Vibrio cholerae	Mutation(s): 0 Gene Names: ERS013166_00020
UniProt
Find proteins for Q9KNG2 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KNG2 Go to UniProtKB: Q9KNG2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KNG2
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.278 (Depositor), 0.239 (DCC)
R-Value Work: 0.220 (Depositor), 0.224 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.526	α = 90
b = 105.526	β = 90
c = 137.755	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-04-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-12
Type: Initial release
Version 1.1: 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.