2CA0 | pdb_00002ca0

Crystal structure of YC-17-bound cytochrome P450 PikC (CYP107L1)

• PDB DOI: https://doi.org/10.2210/pdb2CA0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Streptomyces venezuelae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-12-15 Released: 2006-12-13 
• Deposition Author(s): Yermalitskaya, L.I., Kim, Y., Sherman, D.H., Waterman, M.R., Podust, L.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.338 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Yc-17-Bound Cytochrome P450 Pikc (Cyp107L1)

Yermalitskaya, L.I., Kim, Y., Sherman, D.H., Waterman, M.R., Podust, L.M.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 98.68 kDa 
• Atom Count: 6,269 
• Modeled Residue Count: 786 
• Deposited Residue Count: 872 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 MONOOXYGENASE	A, B	436	Streptomyces venezuelae	Mutation(s): 0  EC: 1.14.15.33
UniProt
Find proteins for O87605 (Streptomyces venezuelae) Explore O87605  Go to UniProtKB:  O87605

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PXI	D [auth A], F [auth B]	4-{[4-(DIMETHYLAMINO)-3-HYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-12-ETHYL-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE C25 H43 N O6 DZGHWPQKGWXOHD-OYZFACIPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.338 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.088	α = 90
b = 91.972	β = 89.92
c = 68.901	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-13 
Deposition Author(s): Yermalitskaya, L.I., Kim, Y., Sherman, D.H., Waterman, M.R., Podust, L.M.

Revision History  

• Version 1.0: 2006-12-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description