3EOL | pdb_00003eol

2.0A crystal structure of isocitrate lyase from Brucella melitensis (P43212)

PDB DOI: https://doi.org/10.2210/pdb3EOL/pdb

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

Deposited: 2008-09-28 Released: 2008-10-21
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.263 (Depositor), 0.282 (DCC)
R-Value Work:
0.221 (Depositor)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of isocitrate lyase from Brucella melitensis

SSGCID

To be published.

Macromolecule Content

Total Structure Weight: 94.72 kDa
Atom Count: 5,848
Modeled Residue Count: 724
Deposited Residue Count: 866
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	433	Brucella melitensis	Mutation(s): 0 Gene Names: BMEI0409 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth B]	D [auth B], E [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain D [auth B] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.263 (Depositor), 0.282 (DCC)
R-Value Work: 0.221 (Depositor)
R-Value Observed: 0.223 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.702	α = 90
b = 79.702	β = 90
c = 281.595	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-10-21

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2008-10-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

3EOL | pdb_00003eol

2.0A crystal structure of isocitrate lyase from Brucella melitensis (P43212)

Literature

Crystal structures of isocitrate lyase from Brucella melitensis

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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