3LHX | pdb_00003lhx

Crystal structure of a Ketodeoxygluconokinase (kdgk) from Shigella flexneri

PDB DOI: https://doi.org/10.2210/pdb3LHX/pdb

Classification: TRANSFERASE
Organism(s): Shigella flexneri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-01-23 Released: 2010-03-02
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.259 (Depositor), 0.260 (DCC)
R-Value Work:
0.215 (Depositor), 0.221 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LHX

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

Literature

Crystal structure of a Ketodeoxygluconokinase (kdgk) from Shigella flexneri

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 70.93 kDa
Atom Count: 4,805
Modeled Residue Count: 595
Deposited Residue Count: 638
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ketodeoxygluconokinase	A, B	319	Shigella flexneri	Mutation(s): 0 Gene Names: kdgK, S4209, SF3557 EC: 2.7.1.45
UniProt
Find proteins for A0A0H2V4A7 (Shigella flexneri) Explore A0A0H2V4A7 Go to UniProtKB: A0A0H2V4A7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2V4A7
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.87 Å
R-Value Free: 0.259 (Depositor), 0.260 (DCC)
R-Value Work: 0.215 (Depositor), 0.221 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.871	α = 90
b = 169.014	β = 90
c = 44.624	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing
SHELXE	model building
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-03-02

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-03-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 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.