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- PDB-7y98: Crystal structure of CYP109B4 from Bacillus Sonorensis in complex... -

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Basic information

Entry
Database: PDB / ID: 7y98
TitleCrystal structure of CYP109B4 from Bacillus Sonorensis in complex with Testosterone
ComponentsCytochrome P450 monooxygenase YjiB
KeywordsOXIDOREDUCTASE / substrate binding / complex
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 / TESTOSTERONE / Cytochrome P450 monooxygenase YjiB
Similarity search - Component
Biological speciesBacillus sonorensis L12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsShen, P.P. / Huang, J.-W. / Li, X. / Liu, W.D. / Chen, C.-C. / Guo, R.-T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2023
Title: Rationally Controlling Selective Steroid Hydroxylation via Scaffold Sampling of a P450 Family
Authors: Zhang, X. / Shen, P. / Zhao, J. / Chen, Y. / Li, X. / Huang, J.W. / Zhang, L. / Li, Q. / Gao, C. / Xing, Q. / Chen, C.C. / Guo, R.T. / Li, A.
History
DepositionJun 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Assembly

Deposited unit
A: Cytochrome P450 monooxygenase YjiB
B: Cytochrome P450 monooxygenase YjiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7926
Polymers92,9822
Non-polymers1,8104
Water3,153175
1
A: Cytochrome P450 monooxygenase YjiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3963
Polymers46,4911
Non-polymers9052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-24 kcal/mol
Surface area18030 Å2
MethodPISA
2
B: Cytochrome P450 monooxygenase YjiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3963
Polymers46,4911
Non-polymers9052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-23 kcal/mol
Surface area17850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.722, 95.703, 78.987
Angle α, β, γ (deg.)90.000, 104.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 monooxygenase YjiB


Mass: 46490.848 Da / Num. of mol.: 2 / Mutation: C40Y,N49S,L264F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sonorensis L12 (bacteria) / Gene: BSONL12_06623 / Plasmid: pRSF-DuetI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M5PFT9
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TES / TESTOSTERONE


Mass: 288.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H28O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
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: 2.86 Å3/Da / Density % sol: 57.06 % / Mosaicity: 1.043 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG 4000, 0.1M Na-Citrate pH 5.6, 20% iso-Propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 19, 2019
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→25 Å / Num. obs: 45487 / % possible obs: 94.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.4
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 4 % / Rmerge(I) obs: 0.725 / Num. unique obs: 4006 / % possible all: 89.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RM4

4rm4


Resolution: 2.27→24.65 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 2005 4.42 %
Rwork0.237 43365 -
obs0.239 45370 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.63 Å2 / Biso mean: 56.54 Å2 / Biso min: 28.11 Å2
Refinement stepCycle: final / Resolution: 2.27→24.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 0 128 175 6389
Biso mean--51.51 50.62 -
Num. residues----751
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.27-2.350.41581730.34134099427289
2.35-2.450.37172160.3144067428389
2.45-2.560.34181740.29444160433490
2.56-2.690.33391840.28984175435990
2.69-2.860.30031920.28654262445493
2.86-3.080.32262090.28044455466496
3.08-3.390.30442160.26234493470998
3.39-3.880.26912130.23074584479798
3.88-4.880.21252150.19544494470997
4.88-24.650.24542130.18754576478997

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