3GG4 | pdb_00003gg4

The crystal structure of glycerol kinase from Yersinia pseudotuberculosis

PDB DOI: https://doi.org/10.2210/pdb3GG4/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pseudotuberculosis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-27 Released: 2009-03-31
Deposition Author(s): Zhang, Z., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.245 (Depositor), 0.203 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3GG4

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

Literature

The crystal structure of glycerol kinase from Yersinia pseudotuberculosis

Zhang, Z., Swaminathan, S., Burley, S.K.

To be published.

Macromolecule Content

Total Structure Weight: 123.89 kDa
Atom Count: 9,004
Modeled Residue Count: 1,070
Deposited Residue Count: 1,108
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerol kinase	A, B	554	Yersinia pseudotuberculosis	Mutation(s): 0 Gene Names: YPTB3592
UniProt
Find proteins for Q665C6 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q665C6 Go to UniProtKB: Q665C6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q665C6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.245 (Depositor), 0.203 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.789	α = 90
b = 110.393	β = 99.13
c = 80.952	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-31

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.