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- PDB-7cl8: Testosterone-bound structure of CYP154C2 from Streptomyces avermi... -

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Basic information

Entry
Database: PDB / ID: 7cl8
TitleTestosterone-bound structure of CYP154C2 from Streptomyces avermitilis in an closed conformation
ComponentsCytochrome P450 hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / hydroxylase / testosterone
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
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / TESTOSTERONE / Cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsXu, L.H. / Fushinobu, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81402810 China
CitationJournal: Appl.Environ.Microbiol. / Year: 2023
Title: Improved 2 alpha-Hydroxylation Efficiency of Steroids by CYP154C2 Using Structure-Guided Rational Design.
Authors: Gao, Q. / Ma, B. / Wang, Q. / Zhang, H. / Fushinobu, S. / Yang, J. / Lin, S. / Sun, K. / Han, B.N. / Xu, L.H.
History
DepositionJul 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5406
Polymers45,2721
Non-polymers1,2675
Water11,530640
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-24 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.740, 61.820, 133.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-978-

HOH

21A-1167-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytochrome P450 hydroxylase / CYP154C2


Mass: 45272.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680) (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) / Strain (production host): BL21 CodonPlus (DE3) RIL / References: UniProt: Q82GL5

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Non-polymers , 5 types, 645 molecules

#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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: hormone*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 640 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.28 %
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: MARMOSAIC 225 mm CCD / Detector: CCD / 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: 1.42→50 Å / Num. obs: 84407 / % possible obs: 99.7 % / Redundancy: 9.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.7
Reflection shellResolution: 1.42→1.5 Å / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 12158 / CC1/2: 0.923 / % possible all: 99.6

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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: 1.42→41.93 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.77 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1609 4316 5.1 %RANDOM
Rwork0.1442 ---
obs0.1451 79964 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.39 Å2 / Biso mean: 15.399 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.42→41.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 88 640 3760
Biso mean--18.63 29 -
Num. residues----400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0133201
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173071
X-RAY DIFFRACTIONr_angle_refined_deg2.0461.6664381
X-RAY DIFFRACTIONr_angle_other_deg1.6341.587089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9185401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.83521.118152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33715496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9391526
X-RAY DIFFRACTIONr_chiral_restr0.1140.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023568
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02646
LS refinement shellResolution: 1.421→1.458 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 353 -
Rwork0.19 5806 -
all-6159 -
obs--99.4 %

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