3GBT | pdb_00003gbt

Crystal structure of gluconate kinase from Lactobacillus acidophilus

PDB DOI: https://doi.org/10.2210/pdb3GBT/pdb

Classification: TRANSFERASE
Organism(s): Lactobacillus acidophilus NCFM
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-20 Released: 2009-03-10
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: 2.40 Å
R-Value Free:
0.231 (Depositor), 0.223 (DCC)
R-Value Work:
0.199 (Depositor), 0.194 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of gluconate kinase from Lactobacillus acidophilus

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

To be published.

Macromolecule Content

Total Structure Weight: 56.13 kDa
Atom Count: 3,932
Modeled Residue Count: 492
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gluconate kinase	A	504	Lactobacillus acidophilus NCFM	Mutation(s): 0 Gene Names: LBA0354 EC: 2.7.1.12
UniProt
Find proteins for Q5FM28 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)) Explore Q5FM28 Go to UniProtKB: Q5FM28
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5FM28
Sequence Annotations Expand
Reference Sequence

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: 2.40 Å
R-Value Free: 0.231 (Depositor), 0.223 (DCC)
R-Value Work: 0.199 (Depositor), 0.194 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.638	α = 90
b = 96.008	β = 93.32
c = 72.94	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

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Entry History

Deposition Data

Released Date: 2009-03-10

Deposition Author(s):

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2009-03-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2024-11-20
Changes: Data collection, Database references, Structure summary

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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.