9BPW | pdb_00009bpw

Crystal Structure of Fumarate Hydratase FumC from Staphylococcus aureus

PDB DOI: https://doi.org/10.2210/pdb9BPW/pdb

Classification: HYDROLASE
Organism(s): Staphylococcus aureus subsp. aureus USA300_FPR3757
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-08 Released: 2025-05-14
Deposition Author(s): Kim, Y., Tesar, C., Endres, M., Babnigg, G., Wong, T., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.215 (Depositor), 0.216 (DCC)
R-Value Work:
0.184 (Depositor), 0.184 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9BPW

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Fumarate Hydratase FumC from Staphylococcus aureus

Kim, Y., Tesar, C., Endres, M., Babnigg, G., Wong, T., Joachimiak, A., Center for Structural Biology of Infectious Diseases (CSBID)

To be published.

Macromolecule Content

Total Structure Weight: 207.18 kDa
Atom Count: 15,253
Modeled Residue Count: 1,844
Deposited Residue Count: 1,844
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fumarate hydratase class II	A, B, C, D	461	Staphylococcus aureus subsp. aureus USA300_FPR3757	Mutation(s): 0 Gene Names: fumC EC: 4.2.1.2
UniProt
Find proteins for Q5HES4 (Staphylococcus aureus (strain COL)) Explore Q5HES4 Go to UniProtKB: Q5HES4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5HES4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FUM Query on FUM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain BA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain BA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain BA [auth D]	BA [auth D], E [auth A], M [auth B], T [auth C]	FUMARIC ACID C₄ H₄ O₄ VZCYOOQTPOCHFL-OWOJBTEDSA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain T [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain O [auth B] SDF format, chain GA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain O [auth B] MOL2 format, chain GA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain O [auth B] mmCIF format, chain GA [auth D]	DA [auth D] EA [auth D] FA [auth D] G [auth A] GA [auth D] DA [auth D], EA [auth D], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain F [auth A] SDF format, chain N [auth B] SDF format, chain U [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] mmCIF format, chain CA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C]	CA [auth D], F [auth A], N [auth B], U [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain CA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain U [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B]	AA [auth C], K [auth A], L [auth A], S [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.215 (Depositor), 0.216 (DCC)
R-Value Work: 0.184 (Depositor), 0.184 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 243.865	α = 90
b = 108.891	β = 116.62
c = 109.023	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-14

Deposition Author(s):

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-05-14
Type: Initial release

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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.