1ZBS | pdb_00001zbs

Crystal Structure of the Putative N-acetylglucosamine Kinase (PG1100) from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR18

PDB DOI: https://doi.org/10.2210/pdb1ZBS/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Porphyromonas gingivalis W83
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-04-08 Released: 2005-11-15
Deposition Author(s): Forouhar, F., Abashidze, M., Kuzin, A., Vorobiev, S.M., Conover, K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.289 (Depositor), 0.301 (DCC)
R-Value Work:
0.231 (Depositor), 0.245 (DCC)
R-Value Observed:
0.231 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of the Putative N-acetylglucosamine Kinase (PG1100) from Porphyromonas gingivalis, Northeast Structural Genomics Target PgR18

Forouhar, F., Abashidze, M., Kuzin, A., Vorobiev, S.M., Conover, K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 32.13 kDa
Atom Count: 2,275
Modelled Residue Count: 283
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein PG1100	A	291	Porphyromonas gingivalis W83	Mutation(s): 6 Gene Names: locus_tag="PG1100"
UniProt
Find proteins for Q7MVG4 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MVG4 Go to UniProtKB: Q7MVG4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MVG4
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.289 (Depositor), 0.301 (DCC)
R-Value Work: 0.231 (Depositor), 0.245 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.506	α = 90
b = 89.506	β = 90
c = 82.323	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
SOLVE	phasing
RESOLVE	phasing
XTALVIEW	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-11-15

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2005-11-15
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.