3I4E | pdb_00003i4e

Crystal structure of Isocitrate Lyase from Burkholderia pseudomallei

PDB DOI: https://doi.org/10.2210/pdb3I4E/pdb

Classification: LYASE
Organism(s): Burkholderia pseudomallei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-07-01 Released: 2009-07-14
Deposition Author(s): Staker, B.L., Arakaki, T., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free:
0.277 (Depositor), 0.280 (DCC)
R-Value Work:
0.213 (Depositor), 0.218 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Isocitrate Lyase from Burkholderia pseudomallei

Staker, B.L., Arakaki, T.

To be published.

Macromolecule Content

Total Structure Weight: 192.51 kDa
Atom Count: 12,730
Modeled Residue Count: 1,648
Deposited Residue Count: 1,756
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A, B, C, D	439	Burkholderia pseudomallei	Mutation(s): 0 Gene Names: aceA, BPSL2188 EC: 4.1.3.1
UniProt
Find proteins for Q63SY3 (Burkholderia pseudomallei (strain K96243)) Explore Q63SY3 Go to UniProtKB: Q63SY3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q63SY3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.277 (Depositor), 0.280 (DCC)
R-Value Work: 0.213 (Depositor), 0.218 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.666	α = 90
b = 137.025	β = 90
c = 160.162	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Refinement description
Version 1.3: 2025-10-22
Changes: 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.