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- PDB-2cpp: HIGH-RESOLUTION CRYSTAL STRUCTURE OF CYTOCHROME P450-CAM -

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Basic information

Entry
Database: PDB / ID: 2cpp
TitleHIGH-RESOLUTION CRYSTAL STRUCTURE OF CYTOCHROME P450-CAM
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
CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.63 Å
AuthorsPoulos, T.L.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: High-resolution crystal structure of cytochrome P450cam.
Authors: Poulos, T.L. / Finzel, B.C. / Howard, A.J.
#1: Journal: J.Biol.Chem. / Year: 1985
Title: The 2.6-Angstroms Crystal Structure of Pseudomonas Putida Cytochrome P450
Authors: Poulos, T.L. / Finzel, B.C. / Gunsalus, I.C. / Wagner, G.C. / Kraut, J.
#2: Journal: Biochemistry / Year: 1986
Title: Crystal Structure of Substrate-Free Pseudomonas Putida Cytochrome P450
Authors: Poulos, T.L. / Finzel, B.C. / Howard, A.J.
#3: Journal: Pept.Protein Rev. / Year: 1984
Title: Heme Enzyme Structure and Function
Authors: Poulos, T.L. / Finzel, B.C.
#4: Journal: J.Biol.Chem. / Year: 1982
Title: Preliminary Crystallographic Data on Cytochrome P450-Cam
Authors: Poulos, T.L. / Perez, M. / Wagner, G.C.
#5: Journal: Biochem.Biophys.Res.Commun. / Year: 1982
Title: The Primary Structure of the Monoxygenase Cytochrome P450-Cam
Authors: Haniu, M. / Armes, L.G. / Tanaka, M. / Yasunobu, K.T. / Shastry, B.S. / Wagner, G.C. / Gunsalus, I.C.
History
DepositionApr 6, 1987Processing site: BNL
SupersessionJul 16, 1987ID: 1CPP
Revision 1.0Jul 16, 1987Provider: 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 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: CYTOCHROME P450-CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3583
Polymers46,5891
Non-polymers7692
Water3,675204
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 89, 100, 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


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


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSOLVENT MOLECULE 515 IS VERY LIKELY A CATION. THIS CONCLUSION IS BASED ON THE OCTAHEDRAL ...SOLVENT MOLECULE 515 IS VERY LIKELY A CATION. THIS CONCLUSION IS BASED ON THE OCTAHEDRAL DISPOSITION OF PEPTIDE AND H2O OXYGEN ATOMS.

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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
Method: other / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMP-450CAM11camphor free
2250 mM11KCl
350 mMdithiothreitol11
466-70 %satammonium sulfate12with 5M KOH

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Data collection

Reflection
*PLUS
Highest resolution: 1.63 Å / Lowest resolution: 2.1 Å / Num. obs: 42513 / % possible obs: 77 % / Observed criterion σ(I): 1 / Num. measured all: 230040 / Rmerge(I) obs: 0.069

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.19 / Highest resolution: 1.63 Å
Refinement stepCycle: LAST / Highest resolution: 1.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 54 204 3462
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.032
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Num. reflection all: 42513 / Num. reflection obs: 34551 / σ(I): 1 / Highest resolution: 1.63 Å / Lowest resolution: 10 Å / Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_planar_d0.050.03
X-RAY DIFFRACTIONp_chiral_restr0.250.3
LS refinement shell
*PLUS
Highest resolution: 1.63 Å / Lowest resolution: 1.7 Å

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