3HN6

Crystal structure of glucosamine-6-phosphate deaminase from Borrelia burgdorferi

PDB DOI: https://doi.org/10.2210/pdb3HN6/pdb

Classification: ISOMERASE
Organism(s): Borreliella burgdorferi B31
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-29 Released: 2009-06-09
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.185
R-Value Observed: 0.188

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Glucosamine-6-phosphate deaminase from Borrelia burgdorferi

Edwards, T.E., Abendroth, J.A., Staker, B.L., Seattle Structural Genomics Center for Infectious Disease

To be published.

Macromolecule Content

Total Structure Weight: 196.66 kDa
Atom Count: 13,486
Modelled Residue Count: 1,610
Deposited Residue Count: 1,734
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, C, D, E A, B, C, D, E, F	289	Borreliella burgdorferi B31	Mutation(s): 0 Gene Names: nagB, BB_0152 EC: 3.5.99.6
UniProt
Find proteins for O30564 (Borreliella burgdorferi (strain ATCC 35210 / DSM 4680 / CIP 102532 / B31)) Explore O30564 Go to UniProtKB: O30564
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O30564
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POP Query on POP Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth C] SDF format, chain I [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth C] mmCIF format, chain I [auth D]	G [auth B], H [auth C], I [auth D]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.9	α = 90
b = 82.79	β = 109.58
c = 126.99	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-06-09

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-06-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3HN6

Crystal structure of glucosamine-6-phosphate deaminase from Borrelia burgdorferi

Crystal Structure of Glucosamine-6-phosphate deaminase from Borrelia burgdorferi

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)