2ZWT | pdb_00002zwt

Crystal Structure of Ferric Cytochrome P450cam

• PDB DOI: https://doi.org/10.2210/pdb2ZWT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-18 Released: 2009-02-17 
• Deposition Author(s): Sakurai, K., Shimada, H., Hayashi, T., Tsukihara, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Substrate binding induces structural changes in cytochrome P450cam

Sakurai, K., Shimada, H., Hayashi, T., Tsukihara, T.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 80-83

• PubMed: 19193991 
• DOI: https://doi.org/10.1107/S1744309108044114
• Primary Citation Related Structures: 
  2ZWT, 2ZWU


• PubMed Abstract: 
  

  The binding of (+)-camphor to cytochrome P450cam (P450cam) expels a cluster of waters at the active site, raising the redox potential of the haem to an extent that allows reduction by the electron-transfer system. This binding was reported to involve no significant structural changes in the protein. Here, two ferric P450cam structures partially complexed with (+)-camphor were determined by X-ray crystallography at 1.30-1.35 A resolution, revealing the structures of the substrate-free and substrate-bound forms. (+)-Camphor binding induces rotation of Thr101 to form a hydrogen bond that acts as a hydrogen donor to a peripheral haem propionate. This bonding contributes to the redox-potential change.

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Organizational Affiliation: 
• Institute for Protein Research, Osaka University, Suita 565-0871, Japan.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 47.65 kDa 
• Atom Count: 4,697 
• Modeled Residue Count: 405 
• Deposited Residue Count: 415 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Camphor 5-monooxygenase	A	415	Pseudomonas putida	Mutation(s): 0  Gene Names: camC EC: 1.14.15.1
UniProt
Find proteins for P00183 (Pseudomonas putida) Explore P00183  Go to UniProtKB:  P00183

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
CAM	C [auth A]	CAMPHOR C10 H16 O DSSYKIVIOFKYAU-XCBNKYQSSA-N
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
K	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.86	α = 90
b = 63.86	β = 90
c = 247.304	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-17 
Deposition Author(s): Sakurai, K., Shimada, H., Hayashi, T., Tsukihara, T.

Revision History  

• Version 1.0: 2009-02-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-06-20
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description