4X8F | pdb_00004x8f

Vibrio cholerae O395 Ribokinase in apo form

PDB DOI: https://doi.org/10.2210/pdb4X8F/pdb

Classification: TRANSFERASE
Organism(s): Vibrio cholerae O395
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-10 Released: 2015-01-21
Deposition Author(s): Paul, R., Patra, M.D., Sen, U.
Funding Organization(s): Department of Atomic Energy, ,Govt. of India, Department of Biotechnology, Govt. of India

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.308 (Depositor), 0.304 (DCC)
R-Value Work:
0.239 (Depositor), 0.237 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Apo and Ligand Bound Vibrio choleraeRibokinase (Vc-RK): Role of Monovalent Cation Induced Activation and Structural Flexibility in Sugar Phosphorylation

Paul, R., Patra, M.D., Sen, U.

(2015) Adv Exp Med Biol 842: 293-307

PubMed: 25408351 Search on PubMed
DOI: https://doi.org/10.1007/978-3-319-11280-0_19
Primary Citation Related Structures:
4X8F, 4XCK, 4XDA

Organizational Affiliation

Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, WB, Kolkata, 700 064, India.

Macromolecule Content

Total Structure Weight: 518.28 kDa
Atom Count: 36,000
Modeled Residue Count: 4,896
Deposited Residue Count: 4,944
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	309	Vibrio cholerae O395	Mutation(s): 0 Gene Names: rbsK, VC0395_0007, VC395_A0124 EC: 2.7.1.15
UniProt
Find proteins for A0A0H2UL04 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A0A0H2UL04 Go to UniProtKB: A0A0H2UL04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2UL04
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.308 (Depositor), 0.304 (DCC)
R-Value Work: 0.239 (Depositor), 0.237 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.22	α = 110.52
b = 130.849	β = 90
c = 145.69	γ = 119.59

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-01-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Atomic Energy, ,Govt. of India	India	--
Department of Biotechnology, Govt. of India	India	--

Revision History (Full details and data files)

Version 1.0: 2015-01-21
Type: Initial release
Version 1.1: 2017-09-27
Changes: Data collection, Derived calculations, Source and taxonomy
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description

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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.