1TXN | pdb_00001txn

Crystal structure of coproporphyrinogen III oxidase

• PDB DOI: https://doi.org/10.2210/pdb1TXN/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-07-05 Released: 2004-11-30 
• Deposition Author(s): Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 

Literature

Crystal structure of coproporphyrinogen III oxidase

Kumaran, D., Swaminathan, S.

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)

Macromolecule Content 

• Total Structure Weight: 76.37 kDa 
• Atom Count: 4,636 
• Modeled Residue Count: 515 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coproporphyrinogen III oxidase	A, B	328	Saccharomyces cerevisiae	Mutation(s): 8  Gene Names: HEM13, YDR044W, YD5112.02 EC: 1.3.3.3
UniProt
Find proteins for P11353 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P11353  Go to UniProtKB:  P11353

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.754	α = 90
b = 71.754	β = 90
c = 117.741	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
HKL-2000	data reduction
SOLVE	phasing
SHARP	phasing
ARP/wARP	model building
CNS	refinement
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-30 
Deposition Author(s): Kumaran, D., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-11-30
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Structure summary