3KZQ | pdb_00003kzq

The crystal structure of the protein with unknown function from Vibrio parahaemolyticus RIMD 2210633

PDB DOI: https://doi.org/10.2210/pdb3KZQ/pdb

Classification: Structural Genomics, Unknown function
Organism(s): Vibrio parahaemolyticus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-12-08 Released: 2010-02-02
Deposition Author(s): Zhang, R., Weger, A., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.218 (Depositor), 0.226 (DCC)
R-Value Work:
0.179 (Depositor), 0.189 (DCC)
R-Value Observed:
0.181 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of the protein with unknown function from Vibrio parahaemolyticus RIMD 2210633

Zhang, R., Weger, A., Shackelford, G., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 146.16 kDa
Atom Count: 11,141
Modeled Residue Count: 1,236
Deposited Residue Count: 1,248
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein VP2116	A, B, C, D, E A, B, C, D, E, F	208	Vibrio parahaemolyticus	Mutation(s): 0 Gene Names: GI:28807109, VP2116
UniProt
Find proteins for Q87MW5 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)) Explore Q87MW5 Go to UniProtKB: Q87MW5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q87MW5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain L [auth C] SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain T [auth E] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain L [auth C] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain T [auth E] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain L [auth C] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A] K [auth B] L [auth C] R [auth E] S [auth E] G [auth A], K [auth B], L [auth C], R [auth E], S [auth E], T [auth E]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C]	M [auth C] N [auth C] O [auth C] P [auth D] Q [auth D] M [auth C], N [auth C], O [auth C], P [auth D], Q [auth D], V [auth F], W [auth F], X [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth F] Interactions & Density Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain U [auth E] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain U [auth E] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain U [auth E] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	H [auth B], I [auth B], J [auth B], U [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain U [auth E] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.218 (Depositor), 0.226 (DCC)
R-Value Work: 0.179 (Depositor), 0.189 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.304	α = 90
b = 118.108	β = 90
c = 206.674	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-02-02

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations