4XDA | pdb_00004xda

Vibrio cholerae O395 Ribokinase complexed with Ribose, ADP and Sodium ion.

PDB DOI: https://doi.org/10.2210/pdb4XDA/pdb

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

Deposited: 2014-12-19 Released: 2015-03-04
Deposition Author(s): Paul, R., Patra, M.D., Sen, U.
Funding Organization(s): Department of Biotechnology, Department of Atomic Energy

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.225 (Depositor), 0.225 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.189 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Crystal Structure of Apo and Ligand Bound Vibrio cholerae Ribokinase (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: 132.25 kDa
Atom Count: 10,337
Modeled Residue Count: 1,224
Deposited Residue Count: 1,236
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribokinase	A, B, C, D	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], I [auth B], L [auth C], O [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D]
RIB Query on RIB Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain E [auth A]	E [auth A], K [auth C], N [auth D]	alpha-D-ribofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-AIHAYLRMSA-N		Interactions Focus chain E [auth A] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth C] Focus chain N [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], P [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.225 (Depositor), 0.225 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.42	α = 106.29
b = 70.7	β = 97.65
c = 79.88	γ = 98.68

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-03-04

Deposition Author(s):

Paul, R.

Patra, M.D.

Sen, U.

Funding Organization	Location	Grant Number
Department of Biotechnology, Department of Atomic Energy	India	MSACR project

Revision History (Full details and data files)

Version 1.0: 2015-03-04
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
Version 2.1: 2024-03-20
Changes: Data collection, Database references, Structure summary

4XDA | pdb_00004xda

Vibrio cholerae O395 Ribokinase complexed with Ribose, ADP and Sodium ion.

Literature

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

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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