3R4I

Crystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERIA XENOVORANS LB400 at 2.24 A resolution

PDB DOI: https://doi.org/10.2210/pdb3R4I/pdb

Classification: LYASE
Organism(s): Paraburkholderia xenovorans LB400
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-03-17 Released: 2011-04-06
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.174
R-Value Work: 0.151
R-Value Observed: 0.153

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERIA XENOVORANS LB400 at 2.24 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 226.02 kDa
Atom Count: 14,805
Modelled Residue Count: 1,914
Deposited Residue Count: 2,034
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Citrate Lyase	A, B, C, D, E A, B, C, D, E, F	339	Paraburkholderia xenovorans LB400	Mutation(s): 0 Gene Names: Bxeno_B0128, Bxe_B2899 EC: 4.1.3.6
UniProt
Find proteins for Q13S43 (Paraburkholderia xenovorans (strain LB400)) Explore Q13S43 Go to UniProtKB: Q13S43
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13S43
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain T [auth D]	O [auth C], T [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain O [auth C] Focus chain T [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain Y [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Y [auth F]	G [auth A] H [auth A] I [auth B] J [auth B] L [auth C] G [auth A], H [auth A], I [auth B], J [auth B], L [auth C], M [auth C], P [auth D], Q [auth D], R [auth D], U [auth E], V [auth E], X [auth F], Y [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F]	K [auth B], N [auth C], S [auth D], W [auth E], Z [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D] Focus chain W [auth E] Focus chain Z [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.174
R-Value Work: 0.151
R-Value Observed: 0.153
Space Group: P 3
Diffraction Data: https://doi.org/10.18430/M33R4I

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.468	α = 90
b = 148.468	β = 90
c = 79.57	γ = 120

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
PHENIX	refinement
XDS	data reduction
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-04-06

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2011-04-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations

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Help and Resources

3R4I

Crystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERIA XENOVORANS LB400 at 2.24 A resolution

Crystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERIA XENOVORANS LB400 at 2.24 A resolution

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)