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- PDB-7y97: Crystal structure of CYP109B4 from Bacillus Sonorensis -

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Basic information

Entry
Database: PDB / ID: 7y97
TitleCrystal structure of CYP109B4 from Bacillus Sonorensis
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 / Cytochrome P450 monooxygenase YjiB
Similarity search - Component
Biological speciesBacillus sonorensis L12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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)94,2154
Polymers92,9822
Non-polymers1,2332
Water1,910106
1
A: Cytochrome P450 monooxygenase YjiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1072
Polymers46,4911
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-24 kcal/mol
Surface area17900 Å2
MethodPISA
2
B: Cytochrome P450 monooxygenase YjiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1072
Polymers46,4911
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-24 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.987, 90.543, 72.029
Angle α, β, γ (deg.)90.000, 102.260, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.47 Å3/Da / Density % sol: 50.14 % / Mosaicity: 1.196 °
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: 2.35→25 Å / Num. obs: 37485 / % possible obs: 99.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.033 / Rrim(I) all: 0.065 / Χ2: 1.633 / Net I/σ(I): 14.7 / Num. measured all: 149002
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.433.90.47937500.8630.2790.5561.399100
2.43-2.533.90.39137380.9090.2270.4521.448100
2.53-2.6540.29937290.950.1730.3461.483100
2.65-2.7940.21437300.9710.1230.2471.552100
2.79-2.9640.15437240.9830.0890.1781.588100
2.96-3.1940.10137490.9920.0580.1161.589100
3.19-3.5140.06637400.9960.0380.0761.736100
3.51-4.0140.04837640.9970.0280.0562.051100
4.01-5.0540.03237650.9990.0180.0371.66899.8
5.05-253.90.0337960.9990.0170.0351.80799.2

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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: 2.36→24.48 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 1895 5.1 %
Rwork0.2175 35278 -
obs0.2195 37173 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.77 Å2 / Biso mean: 61.1124 Å2 / Biso min: 22.62 Å2
Refinement stepCycle: final / Resolution: 2.36→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 86 106 6196
Biso mean--39.79 51 -
Num. residues----741
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 (%)
2.36-2.440.34491910.276335053696100
2.44-2.540.31691920.281834763668100
2.54-2.660.32731900.273535823772100
2.66-2.80.32461910.266434543645100
2.8-2.970.29751910.261135343725100
2.97-3.20.31781910.253335293720100
3.2-3.520.27971900.224735103700100
3.52-4.030.22591870.201335623749100
4.03-5.070.20971870.17635443731100
5.07-24.480.23421850.19733582376799

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