2RI1

Crystal Structure of glucosamine 6-phosphate deaminase (NagB) with GlcN6P from S. mutans

PDB DOI: https://doi.org/10.2210/pdb2RI1/pdb

Classification: HYDROLASE
Organism(s): Streptococcus mutans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-10-10 Released: 2008-03-25
Deposition Author(s): Liu, C., Li, D., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.254
R-Value Work: 0.191
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 52.23 kDa
Atom Count: 4,150
Modelled Residue Count: 470
Deposited Residue Count: 470
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosamine-6-phosphate deaminase	A, B	235	Streptococcus mutans	Mutation(s): 0 Gene Names: SMU.636 EC: 3.5.99.6
UniProt
Find proteins for Q8DV70 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DV70 Go to UniProtKB: Q8DV70
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DV70
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLP Query on GLP Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A]	C [auth A], E [auth B]	2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose C₆ H₁₄ N O₈ P XHMJOUIAFHJHBW-UKFBFLRUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
BTB Query on BTB Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B]	D [auth A], F [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.254
R-Value Work: 0.191
R-Value Observed: 0.194
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.92	α = 90
b = 82.48	β = 90
c = 135.28	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-03-25

Deposition Author(s):

Liu, C.

Li, D.

Su, X.D.

Revision History (Full details and data files)

Version 1.0: 2008-03-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Structure summary

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2RI1

Crystal Structure of glucosamine 6-phosphate deaminase (NagB) with GlcN6P from S. mutans

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)