3OQ8 | pdb_00003oq8

Crystal structure of isocitrate lyase from Brucella melitensis, bound to the product mimic malonate

PDB DOI: https://doi.org/10.2210/pdb3OQ8/pdb

Classification: LYASE
Organism(s): Brucella abortus 2308
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-02 Released: 2010-09-15
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.199 (Depositor), 0.164 (DCC)
R-Value Work:
0.149 (Depositor)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of isocitrate lyase from Brucella melitensis, bound to the product mimic malonate

SSGCID, Gardberg, A., Edwards, T., Staker, B., Stewart, L.

To be published.

Macromolecule Content

Total Structure Weight: 189.9 kDa
Atom Count: 14,231
Modeled Residue Count: 1,692
Deposited Residue Count: 1,732
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate lyase	A, B, C, D	433	Brucella abortus 2308	Mutation(s): 0 Gene Names: BAB1_1631 EC: 4.1.3.1
UniProt
Find proteins for Q2YQA0 (Brucella abortus (strain 2308)) Explore Q2YQA0 Go to UniProtKB: Q2YQA0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2YQA0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain X [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain X [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain X [auth D]	E [auth A], K [auth B], P [auth C], X [auth D]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain X [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain X [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D]	AA [auth D] F [auth A] H [auth A] I [auth A] M [auth B] AA [auth D], F [auth A], H [auth A], I [auth A], M [auth B], N [auth B], R [auth C], S [auth C], T [auth C], V [auth C], Z [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Focus chain Z [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth C] SDF format, chain W [auth C] SDF format, chain Y [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Y [auth D]	BA [auth D] G [auth A] J [auth A] L [auth B] O [auth B] BA [auth D], G [auth A], J [auth A], L [auth B], O [auth B], Q [auth C], U [auth C], W [auth C], Y [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain U [auth C] Focus chain W [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth D] Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain U [auth C] Focus chain W [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.199 (Depositor), 0.164 (DCC)
R-Value Work: 0.149 (Depositor)
R-Value Observed: 0.151 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.5	α = 90
b = 136.03	β = 90
c = 181.77	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2015-04-29
Changes: Non-polymer description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description