3FZ5 | pdb_00003fz5

Crystal structure of possible 2-hydroxychromene-2-carboxylate isomerase from Rhodobacter sphaeroides

• PDB DOI: https://doi.org/10.2210/pdb3FZ5/pdb

• Classification: ISOMERASE
• Organism(s): Cereibacter sphaeroides 2.4.1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-23 Released: 2009-02-03 
• Deposition Author(s): Chang, C., Hatzos, C., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.260 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Crystal structure of possible 2-hydroxychromene-2-carboxylate isomerase from Rhodobacter sphaeroides

Chang, C., Hatzos, C., Freeman, L., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.52 kDa 
• Atom Count: 6,612 
• Modeled Residue Count: 754 
• Deposited Residue Count: 808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible 2-hydroxychromene-2-carboxylate isomerase	A, B, C, D	202	Cereibacter sphaeroides 2.4.1	Mutation(s): 0  Gene Names: RHOS4_04980, RSP_1916 EC: 5.99.1.4
UniProt
Find proteins for Q3J568 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J568  Go to UniProtKB:  Q3J568

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	E [auth A], G [auth B], H [auth C]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
PGE	K [auth D]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	J [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	F [auth A], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	E [auth A], G [auth B], H [auth C]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.260 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.769	α = 94.61
b = 48.724	β = 100.46
c = 95.206	γ = 90.1

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
Coot	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-03 
Deposition Author(s): Chang, C., Hatzos, C., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-02-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary