5TI1 | pdb_00005ti1

Crystal Structure of Fumarylacetoacetate hydrolase from Burkholderia xenovorans LB400

PDB DOI: https://doi.org/10.2210/pdb5TI1/pdb

Classification: HYDROLASE
Organism(s): Paraburkholderia xenovorans LB400
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-09-30 Released: 2017-02-08
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:
0.199 (Depositor), 0.199 (DCC)
R-Value Work:
0.154 (Depositor), 0.154 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Fumarylacetoacetate hydrolase from Burkholderia xenovorans LB400

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Delker, S.L., Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 389.05 kDa
Atom Count: 29,129
Modeled Residue Count: 3,430
Deposited Residue Count: 3,552
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarylacetoacetate hydrolase	A, B, C, D, E A, B, C, D, E, F, G, H	444	Paraburkholderia xenovorans LB400	Mutation(s): 0 Gene Names: Bxe_A3899 EC: 3.7.1.2
UniProt
Find proteins for Q144Z1 (Paraburkholderia xenovorans (strain LB400)) Explore Q144Z1 Go to UniProtKB: Q144Z1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q144Z1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain Y [auth F]	Y [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain Y [auth F] Interactions & Density Focus chain Y [auth F]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain Z [auth F] SDF format, chain V [auth E] SDF format, chain O [auth C] SDF format, chain FA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain Z [auth F] MOL2 format, chain V [auth E] MOL2 format, chain O [auth C] MOL2 format, chain FA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain Z [auth F] mmCIF format, chain V [auth E] mmCIF format, chain O [auth C] mmCIF format, chain FA [auth H]	CA [auth G] FA [auth H] O [auth C] R [auth D] S [auth D] CA [auth G], FA [auth H], O [auth C], R [auth D], S [auth D], V [auth E], Z [auth F]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain FA [auth H] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain FA [auth H] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain Z [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain K [auth B] SDF format, chain W [auth F] SDF format, chain T [auth E] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain I [auth A] SDF format, chain DA [auth H] MOL2 format, chain AA [auth G] MOL2 format, chain K [auth B] MOL2 format, chain W [auth F] MOL2 format, chain T [auth E] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth H] mmCIF format, chain AA [auth G] mmCIF format, chain K [auth B] mmCIF format, chain W [auth F] mmCIF format, chain T [auth E] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth H]	AA [auth G] DA [auth H] I [auth A] K [auth B] M [auth C] AA [auth G], DA [auth H], I [auth A], K [auth B], M [auth C], P [auth D], T [auth E], W [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain AA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain T [auth E] Focus chain W [auth F]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain EA [auth H] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain U [auth E] SDF format, chain X [auth F] SDF format, chain Q [auth D] SDF format, chain BA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain U [auth E] MOL2 format, chain X [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain BA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain U [auth E] mmCIF format, chain X [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain BA [auth G]	BA [auth G] EA [auth H] J [auth A] L [auth B] N [auth C] BA [auth G], EA [auth H], J [auth A], L [auth B], N [auth C], Q [auth D], U [auth E], X [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain BA [auth G] Focus chain EA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain U [auth E] Focus chain X [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.199 (Depositor), 0.199 (DCC)
R-Value Work: 0.154 (Depositor), 0.154 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.9	α = 101.63
b = 83.1	β = 91.17
c = 186.29	γ = 113.81

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
XDS	data scaling
XDS	data reduction
MoRDa	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-02-08

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-02-08
Type: Initial release
Version 1.1: 2017-08-02
Changes: Other, Structure summary
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2025-10-22
Changes: Database references, Structure summary