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- PDB-1cp4: FORMATION, CRYSTAL STRUCTURE, AND REARRANGEMENT OF A CYTOCHROME P... -

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Basic information

Entry
Database: PDB / ID: 1cp4
TitleFORMATION, CRYSTAL STRUCTURE, AND REARRANGEMENT OF A CYTOCHROME P450-CAM IRON-PHENYL COMPLEX
ComponentsCYTOCHROME P450-CAM
KeywordsOXIDOREDUCTASE(OXYGENASE)
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BENZENE / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsRaag, R. / Poulos, T.L.
Citation
Journal: Biochemistry / Year: 1990
Title: Formation, crystal structure, and rearrangement of a cytochrome P-450cam iron-phenyl complex.
Authors: Raag, R. / Swanson, B.A. / Poulos, T.L. / Ortiz de Montellano, P.R.
#1: Journal: To be Published
Title: X-Ray Crystallographic Structural Studies of Cytochrome P450-Cam+
Authors: Raag, R. / Poulos, T.L.
#2: Journal: Biochemistry / Year: 1991
Title: Crystal Structures of Cytochrome P450-Cam Complexed with Camphane, Thiocamphor, and Adamantane: Factors Controlling P450 Substrate Hydroxylation
Authors: Raag, R. / Poulos, T.L.
#3: Journal: Biochemistry / Year: 1989
Title: Crystal Structure of the Carbon Monoxy-Substrate-Cytochrome P450-Cam Ternary Complex
Authors: Raag, R. / Poulos, T.L.
#4: Journal: Biochemistry / Year: 1989
Title: The Structural Basis for Substrate-Induced Changes in Redox Potential and Spin Equilibrium in Cytochrome P450(Cam)
Authors: Raag, R. / Poulos, T.L.
History
DepositionJun 4, 1991Processing site: BNL
Revision 1.0Jan 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2833
Polymers46,5891
Non-polymers6952
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.670, 103.900, 36.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES PRO 89, PRO 100, AND PRO 106 ARE CIS PROLINES.

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Components

#1: Protein CYTOCHROME P450-CAM


Mass: 46588.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-BNZ / BENZENE / Benzene


Mass: 78.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal grow
*PLUS
Temperature: 12-15 ℃ / Method: batch method / Details: took Poulos et al., 1982 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.05 mlprotein11
20.05 mlammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.87 Å / % possible obs: 55 % / Num. measured all: 128716 / Rmerge(I) obs: 0.074

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.199 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 43 209 3467
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.031
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection all: 27666 / Num. reflection obs: 20765 / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_dihedral_angle_d / Dev ideal: 0.036

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