4JJ9 | pdb_00004jj9

Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase

• PDB DOI: https://doi.org/10.2210/pdb4JJ9/pdb

• Classification: ISOMERASE
• Organism(s): Bordetella bronchiseptica RB50
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-03-07 Released: 2013-05-01 
• Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, F., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal Structure of 5-carboxymethyl-2-hydroxymuconate delta-isomerase

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.82 kDa 
• Atom Count: 3,557 
• Modeled Residue Count: 448 
• Deposited Residue Count: 501 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-carboxymethyl-2-hydroxymuconate delta-isomerase	A, B, C	167	Bordetella bronchiseptica RB50	Mutation(s): 0  Gene Names: BB0738, hpaF EC: 5.3.3.10
UniProt
Find proteins for A0A0H3LHY8 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)) Explore A0A0H3LHY8  Go to UniProtKB:  A0A0H3LHY8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth B], F [auth B], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.345	α = 90
b = 75.481	β = 90
c = 107.645	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Eswaramoorthy, S., Chamala, S., Evans, B., Foti, F., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary