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- PDB-1cpt: CRYSTAL STRUCTURE AND REFINEMENT OF CYTOCHROME P450-TERP AT 2.3 A... -

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Basic information

Entry
Database: PDB / ID: 1cpt
TitleCRYSTAL STRUCTURE AND REFINEMENT OF CYTOCHROME P450-TERP AT 2.3 ANGSTROMS RESOLUTION
ComponentsCYTOCHROME P450-TERP
KeywordsOXIDOREDUCTASE(OXYGENASE)
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450-terp
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsHasemann, C.A. / Ravichandran, K.G. / Peterson, J.A. / Deisenhofer, J.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal structure and refinement of cytochrome P450terp at 2.3 A resolution.
Authors: Hasemann, C.A. / Ravichandran, K.G. / Peterson, J.A. / Deisenhofer, J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of P450-Terp and the Hemoprotein Domain of P450-Bm-3, Enzymes Belonging to Two Distinct Classes of the Cytochrome P450 Superfamily
Authors: Boddupalli, S.S. / Hasemann, C.A. / Ravichandran, K.G. / Lu, J.-Y. / Goldsmith, E.J. / Deisenhofer, J. / Peterson, J.A.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Cytochrome P450-Terp: Isolation and Purification of the Protein and Cloning and Sequencing of its Operon
Authors: Peterson, J.A. / Lu, J.-Y. / Geisselsoder, J. / Graham-Lorence, S. / Carmona, C. / Witney, F. / Lorence, M.C.
History
DepositionNov 23, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME P450-TERP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5942
Polymers47,9771
Non-polymers6161
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.440, 69.440, 456.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Atom site foot note1: CIS PROLINE - PRO 108
2: FOR RESIDUE 207 NO DENSITY WAS SEEN FOR SIDE CHAIN ATOMS BEYOND CA.
3: ASPARTATES 236 AND 253 WERE MODELLED IN ALTERNATE CONFORMATIONS.
4: CIS PROLINE - PRO 364 / 5: WATER 440 IS AN AXIAL LIGAND TO THE HEME IRON.

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Components

#1: Protein CYTOCHROME P450-TERP


Mass: 47977.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / References: UniProt: P33006
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3.31 Å3/Da / Density % sol: 62.83 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
220 %PEG125001drop
315 mMDTT1drop
480 mM1dropMgSO4
5200 mM1dropPIPES
620 %PEG125001reservoir
715 mMDTT1reservoir
880 mM1reservoirMgSO4
9200 mM1reservoirPIPES
1P450 terp1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 24645 / % possible obs: 69 % / Num. measured all: 78920 / Rmerge(I) obs: 0.056

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.189 / Rfactor obs: 0.189 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3257 0 43 221 3521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.98
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 6 Å / Num. reflection all: 21470 / Num. reflection obs: 21263 / σ(F): 1 / Rfactor all: 0.205 / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.98
X-RAY DIFFRACTIONx_dihedral_angle_d1.491
X-RAY DIFFRACTIONx_dihedral_angle_deg
X-RAY DIFFRACTIONx_mcbond_it40
X-RAY DIFFRACTIONx_scbond_it41.9

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