3JR2 | pdb_00003jr2

X-ray crystal structure of the Mg-bound 3-keto-L-gulonate-6-phosphate decarboxylase from Vibrio cholerae O1 biovar El Tor str. N16961

PDB DOI: https://doi.org/10.2210/pdb3JR2/pdb

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

Deposited: 2009-09-08 Released: 2009-10-13
Deposition Author(s): Nocek, B., Maltseva, N., Stam, J., Anderson, W., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.202 (Depositor), 0.210 (DCC)
R-Value Work:
0.163 (Depositor), 0.170 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 97.01 kDa
Atom Count: 7,388
Modeled Residue Count: 852
Deposited Residue Count: 872
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	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain BA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth D]	BA [auth D] J [auth A] K [auth A] N [auth B] O [auth B] BA [auth D], J [auth A], K [auth A], N [auth B], O [auth B], T [auth C], U [auth C], V [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], Y [auth D], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain Y [auth D] Focus chain Z [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain I [auth A] SDF format, chain E [auth A] SDF format, chain AA [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain AA [auth D]	AA [auth D], E [auth A], I [auth A], R [auth C], S [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain E [auth A] Focus chain I [auth A] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain AA [auth D] Focus chain E [auth A] Focus chain I [auth A] Focus chain R [auth C] Focus chain S [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain CA [auth D]	CA [auth D] L [auth A] M [auth A] P [auth B] Q [auth B] CA [auth D], L [auth A], M [auth A], P [auth B], Q [auth B], W [auth C], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Focus chain X [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.202 (Depositor), 0.210 (DCC)
R-Value Work: 0.163 (Depositor), 0.170 (DCC)
R-Value Observed: 0.165 (Depositor)

Diffraction Data: https://doi.org/10.18430/m33jr2

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.305	α = 90
b = 95.711	β = 90
c = 125.577	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-02-08
Changes: Database references, Structure summary
Version 1.3: 2018-01-24
Changes: Structure summary
Version 1.4: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2023-11-22
Changes: Data collection
Version 1.6: 2024-11-06
Changes: Structure summary