5HJ5 | pdb_00005hj5

Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from Vibrio cholerae with BETA-D-GLUCOSE-6-PHOSPHATE and FRUCTOSE-6-PHOSPHATE

PDB DOI: https://doi.org/10.2210/pdb5HJ5/pdb

Classification: HYDROLASE
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-01-12 Released: 2016-02-03
Deposition Author(s): Chang, C., Maltseva, N., Kim, Y., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.170 (Depositor), 0.171 (DCC)
R-Value Work:
0.135 (Depositor), 0.136 (DCC)
R-Value Observed:
0.137 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of tertiary complex of glucosamine-6-phosphate deaminase from Vibrio cholerae with BETA-D-GLUCOSE-6-PHOSPHATE and FRUCTOSE -6-PHOSPHATE

Chang, C., Maltseva, N., Kim, Y., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 121.66 kDa
Atom Count: 10,140
Modeled Residue Count: 1,065
Deposited Residue Count: 1,068
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosamine-6-phosphate deaminase	A, B, C, D	267	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: nagB, VC_A1025 EC: 3.5.99.6
UniProt
Find proteins for Q9KKS5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KKS5 Go to UniProtKB: Q9KKS5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KKS5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BG6 Query on BG6 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D]	F [auth A], K [auth B], O [auth C], R [auth D]	6-O-phosphono-beta-D-glucopyranose C₆ H₁₃ O₉ P NBSCHQHZLSJFNQ-VFUOTHLCSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain R [auth D]
F6R Query on F6R Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	E [auth A], J [auth B], N [auth C], Q [auth D]	FRUCTOSE -6-PHOSPHATE C₆ H₁₃ O₉ P GSXOAOHZAIYLCY-HSUXUTPPSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain Q [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D]	G [auth A] H [auth A] I [auth A] M [auth B] P [auth C] G [auth A], H [auth A], I [auth A], M [auth B], P [auth C], S [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D]
ACY Query on ACY 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]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.170 (Depositor), 0.171 (DCC)
R-Value Work: 0.135 (Depositor), 0.136 (DCC)
R-Value Observed: 0.137 (Depositor)

Diffraction Data:

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.093	α = 90
b = 113.093	β = 90
c = 215.683	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
Coot	model building
SBC-Collect	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-02-03

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-02-03
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary