Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 47396.70 
• Atom Count: 3263 
• Residue Count: 414 
• Unique protein chains: 1

1YRC

X-ray Crystal Structure of hydrogenated Cytochrome P450cam

• DOI: 10.2210/pdb1YRC/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2005-02-03 Released: 2005-02-15 
• Deposition Author(s): Meilleur, F., Dauvergne, M.-T., Schlichting, I., Myles, D.A.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.219 
• R-Value Work: 0.202 

Literature

Production and X-ray crystallographic analysis of fully deuterated cytochrome P450cam.

Meilleur, F., Dauvergne, M.T., Schlichting, I., Myles, D.A.

(2005) Acta Crystallogr.,Sect.D 61: 539-544

• PubMed: 15858263 
• DOI: 10.1107/S0907444905003872
• Primary Citation of Related Structures:  
  1YRD


• PubMed Abstract: 
  

Neutron protein crystallography allows H-atom positions to be located in biological structures at the relatively modest resolution of 1.5-2.0 A. A difficulty of this technique arises from the incoherent scattering from hydrogen, which considerably reduces the signal-to-noise ratio of the data. This can be overcome by preparing fully deuterated samples. Efficient protocols for routine and low-cost production of in vivo deuterium-enriched proteins have been developed. Here, the overexpression and crystallization of highly (>99%) deuterium-enriched cytochrome P450cam for neutron analysis is reported. Cytochrome P450cam from Pseudomonas putida catalyses the hydroxylation of camphor from haem-bound molecular O(2) via a mechanism that is thought to involve a proton-shuttle pathway to the active site. Since H atoms cannot be visualized in available X-ray structures, neutron diffraction is being used to determine the protonation states and water structure at the active site of the enzyme. Analysis of both hydrogenated and perdeuterated P450cam showed no significant changes between the X-ray structures determined at 1.4 and 1.7 A, respectively. This work demonstrates that the fully deuterated protein is highly isomorphous with the native (hydrogenated) protein and is appropriate for neutron protein crystallographic analysis.

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Organizational Affiliation: 

European Molecular Laboratory Grenoble Outstation, 6 Rue Jules Horowitz, 38042 Grenoble, France. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cytochrome P450-cam	A	414	Pseudomonas putida	Mutation(s): 0  Gene Names: camC (cyp101) EC: 1.14.15.1
Find proteins for P00183 (Pseudomonas putida) Go to UniProtKB:  P00183

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
K	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CAM	A	CAMPHOR C10 H16 O DSSYKIVIOFKYAU-XCBNKYQSSA-N
HEM	A	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.4 Å
• R-Value Free: 0.219 
• R-Value Work: 0.202 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 63.650	α = 90.00
b = 63.650	β = 90.00
c = 246.490	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-03 
• Released Date: 2005-02-15 
• Deposition Author(s): Meilleur, F., Dauvergne, M.-T., Schlichting, I., Myles, D.A.A.

Revision History 

• Version 1.0: 2005-02-15
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance