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- PDB-1eup: X-RAY CRYSTAL STRUCTURE OF CYTOCHROME P450ERYF WITH ANDROSTENDION... -

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Basic information

Entry
Database: PDB / ID: 1eup
TitleX-RAY CRYSTAL STRUCTURE OF CYTOCHROME P450ERYF WITH ANDROSTENDIONE BOUND
ComponentsCYTOCHROME P450ERYF
KeywordsOXIDOREDUCTASE / cytochrome P450 / steroid / androstenedione / cytochrome P450eryF
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
4-ANDROSTENE-3-17-DIONE / 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. / Anderson, R. / Hatziris, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structures of ligand complexes of P450eryF exhibiting homotropic cooperativity.
Authors: Cupp-Vickery, J. / Anderson, R. / Hatziris, Z.
History
SupersessionApr 17, 2000ID: 1EH0
DepositionApr 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
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_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 P450ERYF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7044
Polymers44,5151
Non-polymers1,1893
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.154, 79.114, 99.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME P450ERYF


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-ASD / 4-ANDROSTENE-3-17-DIONE


Mass: 286.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26O2 / Comment: hormone*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000 NaAc Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
124 %PEG40001reservoir
20.2 M1reservoirNaAc
30.1 MTris-HCl1reservoirpH8.5
40.400 mMprotein1drop
50.800 mMandrostenedione1dropor 9-aminophenanthrene 0.400mM

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Data collection

DiffractionMean temperature: 22 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 24521 / Num. obs: 23549 / % possible obs: 95.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10
Reflection
*PLUS
Num. measured all: 133137

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.1→10 Å / σ(F): 2
RfactorNum. reflection% reflection
all0.184 --
obs0.184 23549 95.5 %
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 85 331 3555
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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