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- PDB-7y9o: Crystal structure of a CYP109B4 variant from Bacillus sonorensis -

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Basic information

Entry
Database: PDB / ID: 7y9o
TitleCrystal structure of a CYP109B4 variant from Bacillus sonorensis
ComponentsCytochrome P450 monooxygenase YjiB
KeywordsOXIDOREDUCTASE / Synthesis / Monooxygenase
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 / IMIDAZOLE / Cytochrome P450 monooxygenase YjiB
Similarity search - Component
Biological speciesBacillus sonorensis L12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsShen, P.P. / Huang, J.-W. / Li, X. / Liu, W.D. / Chen, C.-C. / Guo, R.-T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
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 25, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2755
Polymers46,5091
Non-polymers7664
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-24 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.870, 62.602, 140.526
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450 monooxygenase YjiB


Mass: 46508.797 Da / Num. of mol.: 1
Mutation: C40Y/N49S/L264F/L240V/S387F/V84L/V292S/I291T/M290F/F294I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sonorensis L12 (bacteria) / Gene: BSONL12_06623 / 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.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M calcium acetate hydrate, 0.1M Tris (pH 7.0), 18% Polyethylene glycol 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Dec 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.84→38.06 Å / Num. obs: 37491 / % possible obs: 99.8 % / Redundancy: 8.04 % / Rmerge(I) obs: 0.0769 / Net I/σ(I): 15.9
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 3.69 % / Rmerge(I) obs: 0.3271 / Num. unique obs: 1732 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SAINTdata reduction
SAINTdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RM4

4rm4


Resolution: 1.84→38.06 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.313 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1850 5 %RANDOM
Rwork0.1905 ---
obs0.1921 35384 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.95 Å2 / Biso mean: 25.917 Å2 / Biso min: 11.98 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.84→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 50 472 3683
Biso mean--18.63 37.7 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133300
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153119
X-RAY DIFFRACTIONr_angle_refined_deg1.621.674479
X-RAY DIFFRACTIONr_angle_other_deg1.3941.5937198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5875392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.1122.139187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40115579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1681525
X-RAY DIFFRACTIONr_chiral_restr0.0860.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023716
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02770
LS refinement shellResolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 146 -
Rwork0.287 2530 -
all-2676 -
obs--98.13 %

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