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- PDB-7cl9: Androstenedione-bound structure of CYP154C2 from Streptomyces ave... -

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Basic information

Entry
Database: PDB / ID: 7cl9
TitleAndrostenedione-bound structure of CYP154C2 from Streptomyces avermitilis in an open conformation
ComponentsCytochrome P450 hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / hydroxylase / Androstenedione
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
4-ANDROSTENE-3-17-DIONE / PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesStreptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsXu, L.H. / Fushinobu, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81402810 China
CitationJournal: To Be Published
Title: Androstenedione-bound structure of CYP154C2 from Streptomyces avermitilis in an open conformation
Authors: Xu, L.H. / Fushinobu, S.
History
DepositionJul 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 2.0Sep 20, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_detector / entity / entity_src_gen / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_detector.detector / _diffrn_detector.type / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _refine.B_iso_max / _refine.B_iso_min / _refine.details / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.pdbx_ls_sigma_F / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.number_reflns_all / _struct_conn.ptnr2_label_asym_id
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Nov 29, 2023Group: 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 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1104
Polymers43,1011
Non-polymers1,0093
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-24 kcal/mol
Surface area17600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.600, 80.130, 120.630
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 P450 hydroxylase / CYP154C2


Mass: 43101.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis MA-4680 = NBRC 14893 (bacteria)
Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680
Gene: cyp19, SAVERM_3882 / Production host: Escherichia coli (E. coli) / References: UniProt: Q82GL5
#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.: 1 / Source method: obtained synthetically / Formula: C19H26O2 / Comment: hormone*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.06 Å3/Da / Density % sol: 59.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.06 M Divalents, 0.1 M Buffer System 2 pH 7.5, 50% v/v Precipitant mix 1

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 39415 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 5656 / CC1/2: 0.851 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L69

6l69


Resolution: 1.95→49.79 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.178 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 2001 5.1 %RANDOM
Rwork0.19208 ---
obs0.19495 37351 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.571 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.95→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 71 304 3392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133159
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173014
X-RAY DIFFRACTIONr_angle_refined_deg1.621.6664333
X-RAY DIFFRACTIONr_angle_other_deg1.3691.586954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56321.118152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04615490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9151526
X-RAY DIFFRACTIONr_chiral_restr0.0770.2420
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023551
X-RAY DIFFRACTIONr_gen_planes_other0.010.02643
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6984.1191591
X-RAY DIFFRACTIONr_mcbond_other3.6964.1151589
X-RAY DIFFRACTIONr_mcangle_it5.0776.1721987
X-RAY DIFFRACTIONr_mcangle_other5.0766.1711987
X-RAY DIFFRACTIONr_scbond_it4.3264.4951568
X-RAY DIFFRACTIONr_scbond_other4.3244.4951569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3436.5982347
X-RAY DIFFRACTIONr_long_range_B_refined8.15150.1343647
X-RAY DIFFRACTIONr_long_range_B_other8.15449.7523568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 140 -
Rwork0.31 2707 -
obs--100 %

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