1SDQ | pdb_00001sdq

Structure of reduced-NO adduct of mesopone cytochrome c peroxidase

• PDB DOI: https://doi.org/10.2210/pdb1SDQ/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-02-13 Released: 2005-07-12 
• Deposition Author(s): Bhaskar, B., Immoos, C.E., Sulc, F., Cohem, M.S., Farmer, P.J., Poulos, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of resting (Fe3+), reduced (Fe2+) and NO-bound states of mesopone cytochrome c peroxidase (MpCcP) (R-isomer)

Bhaskar, B., Immoos, C.E., Sulc, F., Cohem, M.S., Farmer, P.J., Poulos, T.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.24 kDa 
• Atom Count: 2,986 
• Modeled Residue Count: 294 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c peroxidase, mitochondrial	A	294	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: CCP1, CCP, CPO, YKR066C, OBPYC EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00431  Go to UniProtKB:  P00431

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMI	B [auth A]	FE-(4-MESOPORPHYRINONE)-R-ISOMER C34 H36 Fe N4 O5 RRFOXEHBNIETRO-MDYNBEAQSA-L
NO	C [auth A]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.884	α = 90
b = 75.625	β = 90
c = 50.958	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-12 
Deposition Author(s): Bhaskar, B., Immoos, C.E., Sulc, F., Cohem, M.S., Farmer, P.J., Poulos, T.L.

Revision History  

• Version 1.0: 2005-07-12
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description