5IQJ | pdb_00005iqj

1.9 Angstrom Crystal Structure of Protein with Unknown Function from Vibrio cholerae.

PDB DOI: https://doi.org/10.2210/pdb5IQJ/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Vibrio cholerae O1 biovar El Tor
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2016-03-10 Released: 2016-03-23
Deposition Author(s): Minasov, G., Wawrzak, Z., Stogios, P.J., Skarina, T., Seed, K.D., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.229 (Depositor), 0.234 (DCC)
R-Value Work:
0.181 (Depositor), 0.189 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5IQJ

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

Literature

1.9 Angstrom Crystal Structure of Protein with Unknown Function from Vibrio cholerae.

Minasov, G., Wawrzak, Z., Stogios, P.J., Skarina, T., Seed, K.D., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases

To be published.

Macromolecule Content

Total Structure Weight: 46.42 kDa
Atom Count: 3,768
Modeled Residue Count: 387
Deposited Residue Count: 402
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C	134	Vibrio cholerae O1 biovar El Tor	Mutation(s): 0
UniProt
Find proteins for M1QWM5 (Vibrio cholerae serotype O1 biovar El Tor) Explore M1QWM5 Go to UniProtKB: M1QWM5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	M1QWM5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
TTN Query on TTN Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain S [auth C]	G [auth A], S [auth C]	TARTRONATE C₃ H₂ O₅ ROBFUDYVXSDBQM-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain S [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] MOL2 format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] mmCIF format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C]	F [auth A], O [auth B], P [auth B], R [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Interactions & Density Focus chain F [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain Q [auth C] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C]	J [auth B], Q [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain Q [auth C] Interactions & Density Focus chain J [auth B] Focus chain Q [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.229 (Depositor), 0.234 (DCC)
R-Value Work: 0.181 (Depositor), 0.189 (DCC)
R-Value Observed: 0.183 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.126	α = 90
b = 149.512	β = 90
c = 159.966	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-03-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-03-23
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

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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.