2HPD | pdb_00002hpd

CRYSTAL STRUCTURE OF HEMOPROTEIN DOMAIN OF P450BM-3, A PROTOTYPE FOR MICROSOMAL P450'S

• PDB DOI: https://doi.org/10.2210/pdb2HPD/pdb

• Classification: OXIDOREDUCTASE(OXYGENASE)
• Organism(s): Priestia megaterium
• Mutation(s): No 


• Deposited: 1993-09-16 Released: 1993-10-31 
• Deposition Author(s): Ravichandran, K.G., Boddupalli, S.S., Hasemann, C.A., Peterson, J.A., Deisenhofer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 
  0.167 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450's.

Ravichandran, K.G., Boddupalli, S.S., Hasermann, C.A., Peterson, J.A., Deisenhofer, J.

(1993) Science 261: 731-736

• PubMed: 8342039 
• DOI: https://doi.org/10.1126/science.8342039
• Primary Citation Related Structures: 
  2HPD


• PubMed Abstract: 
  

  Cytochrome P450BM-3, a bacterial fatty acid monoxygenase, resembles the eukaryotic microsomal P450's and their flavoprotein reductase in primary structure and function. The three-dimensional structure of the hemoprotein domain of P450BM-3 was determined by x-ray diffraction and refined to an R factor of 16.9 percent at 2.0 angstrom resolution. The structure consists of an alph and a beta domain. The active site heme is accessible through a long hydrophobic channel formed primarily by the beta domain and the B' and F helices of the alpha domain. The two molecules in the asymmetric unit differ in conformation around the substrate binding pocket. Substantial differences between P450BM-3 and P450cam, the only other P450 structure available, are observed around the substrate binding pocket and the regions important for redox partner binding. A general mechanism for proton transfer in P450's is also proposed.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75235-9050.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.83 kDa 
• Atom Count: 7,897 
• Modeled Residue Count: 914 
• Deposited Residue Count: 942 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 BM-3	A, B	471	Priestia megaterium	Mutation(s): 0  EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (UniProt)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779  Go to UniProtKB:  P14779

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work:  0.167 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.4	α = 90
b = 154	β = 94.7
c = 62.2	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Ravichandran, K.G., Boddupalli, S.S., Hasemann, C.A., Peterson, J.A., Deisenhofer, J.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Other