3IEB | pdb_00003ieb

Crystal structure of 3-keto-L-gulonate-6-phosphate decarboxylase from Vibrio cholerae O1 biovar El Tor str. N16961

PDB DOI: https://doi.org/10.2210/pdb3IEB/pdb

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

Deposited: 2009-07-22 Released: 2009-08-18
Deposition Author(s): Nocek, B., Maltseva, N., Osipiuk, J., Stam, J., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.208 (Depositor), 0.218 (DCC)
R-Value Work:
0.178 (Depositor), 0.191 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of 3-keto-L-gulonate-6-phosphate decarboxylase from Vibrio cholerae O1 biovar El Tor str. N16961

Nocek, B., Maltseva, N., Osipiuk, J., Stam, J., Anderson, W., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 121.68 kDa
Atom Count: 8,970
Modelled Residue Count: 1,068
Deposited Residue Count: 1,090
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hexulose-6-phosphate synthase SgbH	A, B, C, D, E	218	Vibrio cholerae	Mutation(s): 0 Gene Names: VC_A0242
UniProt
Find proteins for Q9KMS8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KMS8 Go to UniProtKB: Q9KMS8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KMS8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain F [auth A] SDF format, chain FA [auth E] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D]	AA [auth D] DA [auth E] EA [auth E] F [auth A] FA [auth E] AA [auth D], DA [auth E], EA [auth E], F [auth A], FA [auth E], H [auth A], I [auth A], J [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], U [auth C], X [auth D], Y [auth D], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain F [auth A] Focus chain FA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain F [auth A] Focus chain FA [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D]	BA [auth E] CA [auth E] G [auth A] K [auth B] L [auth B] BA [auth E], CA [auth E], G [auth A], K [auth B], L [auth B], M [auth B], P [auth C], Q [auth C], V [auth D], W [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.208 (Depositor), 0.218 (DCC)
R-Value Work: 0.178 (Depositor), 0.191 (DCC)
R-Value Observed: 0.180 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33ieb

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.398	α = 90
b = 157.398	β = 90
c = 303.392	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
REFMAC	refinement
HKL-3000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-08-18

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary