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- PDB-6l69: Crystal structure of CYP154C2 from Streptomyces avermitilis -

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Basic information

Entry
Database: PDB / ID: 6l69
TitleCrystal structure of CYP154C2 from Streptomyces avermitilis
ComponentsCytochrome P450 hydroxylase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / substrate-free / hydroxylase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 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 / Cytochrome P450 hydroxylase
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsXu, L.H. / Fushinobu, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Regio- and stereoselective hydroxylation of testosterone by a novel cytochrome P450 154C2 from Streptomyces avermitilis.
Authors: Wang, Q. / Ma, B. / Fushinobu, S. / Zhang, C. / Xu, L.H.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Overview of refinement procedures within REFMAC5: utilizing data from different sources.
Authors: Kovalevskiy, O. / Nicholls, R.A. / Long, F. / Carlon, A. / Murshudov, G.N.
History
DepositionOct 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 hydroxylase
B: Cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7784
Polymers90,5452
Non-polymers1,2332
Water13,493749
1
A: Cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8892
Polymers45,2721
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-25 kcal/mol
Surface area16060 Å2
MethodPISA
2
B: Cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8892
Polymers45,2721
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-25 kcal/mol
Surface area16220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.780, 53.390, 98.581
Angle α, β, γ (deg.)90.000, 90.040, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Cytochrome P450 hydroxylase


Mass: 45272.414 Da / Num. of mol.: 2
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: unidentified plasmid (others) / References: UniProt: Q82GL5
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 749 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 6.5), 28% PEGMME 2000

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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: 1.5→50 Å / Num. obs: 112411 / % possible obs: 99.5 % / Redundancy: 6 % / Biso Wilson estimate: 9.27 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.2
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 16190

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GWI

1gwi


Resolution: 1.5→33.89 Å / SU ML: 0.1292 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.9099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1928 5724 5.09 %
Rwork0.1678 106647 -
obs0.1691 112371 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.14 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6034 0 86 749 6869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00646258
X-RAY DIFFRACTIONf_angle_d0.98798578
X-RAY DIFFRACTIONf_chiral_restr0.05141000
X-RAY DIFFRACTIONf_plane_restr0.00631114
X-RAY DIFFRACTIONf_dihedral_angle_d8.24213752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.24331830.21153535X-RAY DIFFRACTION98.36
1.52-1.530.22222150.20673442X-RAY DIFFRACTION98.36
1.53-1.550.26151760.2123489X-RAY DIFFRACTION99.05
1.55-1.570.2121600.19923554X-RAY DIFFRACTION97.74
1.57-1.590.25261970.1963504X-RAY DIFFRACTION99.33
1.59-1.620.20491770.18753549X-RAY DIFFRACTION98.47
1.62-1.640.17061710.18523509X-RAY DIFFRACTION99.65
1.64-1.660.21461780.18313536X-RAY DIFFRACTION98.96
1.66-1.690.21762100.17853507X-RAY DIFFRACTION99.33
1.69-1.720.20951740.17393529X-RAY DIFFRACTION99.41
1.72-1.750.1941750.16933577X-RAY DIFFRACTION99.39
1.75-1.780.19982010.17273550X-RAY DIFFRACTION99.23
1.78-1.810.22411690.16373551X-RAY DIFFRACTION99.79
1.81-1.850.21231730.17173540X-RAY DIFFRACTION99.12
1.85-1.890.19641810.16123563X-RAY DIFFRACTION99.36
1.89-1.930.21421810.15993561X-RAY DIFFRACTION99.63
1.93-1.980.20272320.15513532X-RAY DIFFRACTION99.71
1.98-2.040.19731960.15713518X-RAY DIFFRACTION99.97
2.04-2.10.1841920.1563554X-RAY DIFFRACTION99.84
2.1-2.160.17831720.15413573X-RAY DIFFRACTION99.95
2.16-2.240.16961790.15253620X-RAY DIFFRACTION99.95
2.24-2.330.17582170.15343567X-RAY DIFFRACTION100
2.33-2.440.19691940.15753536X-RAY DIFFRACTION99.23
2.44-2.560.19872170.16923544X-RAY DIFFRACTION99.97
2.56-2.730.22191640.16743648X-RAY DIFFRACTION100
2.73-2.940.16982090.15913552X-RAY DIFFRACTION99.97
2.94-3.230.1711760.15883627X-RAY DIFFRACTION99.97
3.23-3.70.18042020.15843574X-RAY DIFFRACTION99.55
3.7-4.660.16152260.15373616X-RAY DIFFRACTION100

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