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- PDB-1oxa: CYTOCHROME P450 (DONOR:O2 OXIDOREDUCTASE) -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1oxa
TitleCYTOCHROME P450 (DONOR:O2 OXIDOREDUCTASE)
ComponentsCYTOCHROME P450 ERYF
KeywordsOXIDOREDUCTASE (OXYGENASE)
Function / homology
Function and homology information


6-deoxyerythronolide B hydroxylase / erythromycin biosynthetic process / 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
6-DEOXYERYTHRONOLIDE B / PROTOPORPHYRIN IX CONTAINING FE / 6-deoxyerythronolide B hydroxylase
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsCupp-Vickery, J.R. / Poulos, T.L.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of cytochrome P450eryF involved in erythromycin biosynthesis.
Authors: Cupp-Vickery, J.R. / Poulos, T.L.
#1: Journal: Proteins / Year: 1994
Title: Preliminary Crystallographic Analysis of an Enzyme Involved in Erythromycin Biosynthesis: Cytochrome P450Eryf
Authors: Cupp-Vickery, J.R. / Li, H. / Poulos, T.L.
History
DepositionJul 14, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_ref_seq_dif / 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_ref_seq_dif.details / _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 ERYF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5183
Polymers44,5151
Non-polymers1,0032
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.160, 79.670, 99.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 96

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Components

#1: Protein CYTOCHROME P450 ERYF


Mass: 44515.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharopolyspora erythraea (bacteria) / References: UniProt: Q00441
#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-DEB / 6-DEOXYERYTHRONOLIDE B


Mass: 386.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H38O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.95 %
Description: TWO DERIVATIVE DATA SETS WERE ACQUIRED WITH A SIEMENS X-1000 AREA DETECTOR AND A ROTATING ANODE EQUIPPED WITH FOCUSING, MIRROR OPTICS. A NATIVE DATA SET WAS COLLECTED WITH TWO MARK III ...Description: TWO DERIVATIVE DATA SETS WERE ACQUIRED WITH A SIEMENS X-1000 AREA DETECTOR AND A ROTATING ANODE EQUIPPED WITH FOCUSING, MIRROR OPTICS. A NATIVE DATA SET WAS COLLECTED WITH TWO MARK III AREA DETECTORS AND A RIGAKU ROTATING ANODE AT THE UNIVERSITY OF CALIFORNIA, SAN DIEGO, U.S.A.
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124 %PEG40001reservoir
20.2 Msodium acetate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 23771 / % possible obs: 91 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.0538
Reflection
*PLUS
Num. measured all: 127949 / Rmerge(I) obs: 0.0538

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
SDMSdata reduction
X-PLORphasing
RefinementResolution: 2.1→10 Å / Rfactor Rwork: 0.196 / Rfactor obs: 0.196 / σ(F): 0
Details: RESIDUES 160 - 166 WERE NOT VISIBLE IN THE ELECTRON DENSITY. RESIDUE NUMBER 1 IS NOT VISIBLE.
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 70 241 3450
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.342
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
Solvent computation
*PLUS
Displacement parameters
*PLUS

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