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- PDB-1jin: P450eryF/ketoconazole -

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Basic information

Entry
Database: PDB / ID: 1jin
TitleP450eryF/ketoconazole
ComponentsCYTOCHROME P450 107A1
KeywordsHYDROLASE / cytochrome P450 / P450 / P450eryF / ketoconazole / azole drug
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
PROTOPORPHYRIN IX CONTAINING FE / Chem-KTN / 6-deoxyerythronolide B hydroxylase
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCupp-Vickery, J.R. / Garcia, C. / Hofacre, A. / McGee-Estrada, K.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Ketoconazole-induced conformational changes in the active site of cytochrome P450eryF.
Authors: Cupp-Vickery, J.R. / Garcia, C. / Hofacre, A. / McGee-Estrada, K.
History
DepositionJul 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME P450 107A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6633
Polymers44,5151
Non-polymers1,1482
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.228, 79.738, 99.364
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME P450 107A1 / 6-DEOXYERYTHRONOLIDE B HYDROXYLASE / ERYTHOMYCIN A BIOSYNTHESIS HYDROLASE


Mass: 44515.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109DE3 / References: UniProt: Q00441, Oxidoreductases
#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-KTN / CIS-1-ACETYL-4-(4-((2-(2,4-DICHLOROPHENYL)-2-(1H-IMIDAZOL-1-YLMETHYL)-1,3-DIOXOLAN-4-YL)METHOXY)PHENYL)PIPERAZINE / KETOCONAZOLE


Mass: 531.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28Cl2N4O4 / Comment: medication, antifungal*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 48.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Peg 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122 %(w/v)PEG40001reservoir
20.2 Msodium acetate1reservoir
30.1 MTris-HCl1reservoirpH8.5
40.400 mMketoconazole1drop

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 19771 / Num. obs: 18985 / % possible obs: 96 % / Observed criterion σ(F): 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Num. obs: 24065 / % possible obs: 99.2 % / Num. measured all: 133137 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 93.1 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P450eryF without substrate

Resolution: 2.3→50 Å / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1906 -10% of data
Rwork0.184 ---
obs0.184 18985 96 %-
all-19771 --
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 79 251 3469
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / % reflection Rfree: 10 % / Rfactor obs: 0.194 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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