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- PDB-7jw5: Crystal structure of WT-CYP199A4 in complex with 4-phenylbenzoic acid -

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Basic information

Entry
Database: PDB / ID: 7jw5
TitleCrystal structure of WT-CYP199A4 in complex with 4-phenylbenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome / bacterial P450 / 4-phenylbenzoic acid
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 / biphenyl-4-carboxylic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.526 Å
AuthorsLee, J.H.Z. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: Acs Catalysis / Year: 2022
Title: Different Geometric Requirements for Cytochrome P450-Catalyzed Aliphatic Versus Aromatic Hydroxylation Results in Chemoselective Oxidation
Authors: Coleman, T. / Kirk, A.M. / Lee, J.H.Z. / Doherty, D.Z. / Bruning, J.B. / Krenske, E.H. / De Voss, J.J. / Bell, S.G.
History
DepositionAug 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 18, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4384
Polymers44,5871
Non-polymers8503
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-37 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.513, 51.486, 78.725
Angle α, β, γ (deg.)90.000, 92.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 44587.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain HaA2) (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02, Oxidoreductases
#2: Chemical ChemComp-Z7Z / biphenyl-4-carboxylic acid


Mass: 198.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M magnesium acetate, 100 mM Bis-Tris (adjusted with acetic acid to pH 5.0-5.75), 20-32 % w/v PEG3350
PH range: 5.0-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.526→44.482 Å / Num. obs: 53158 / % possible obs: 97.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.53-1.555.51.4661298123650.4320.6691.6160.887.8
8.35-44.486.30.03323063660.9990.0140.03635.299.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.82 Å44.48 Å
Translation5.82 Å44.48 Å

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASER2.7.17phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVB

5uvb


Resolution: 1.526→44.482 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 1990 3.75 %
Rwork0.1658 51138 -
obs0.167 53128 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.57 Å2 / Biso mean: 20.1911 Å2 / Biso min: 10.02 Å2
Refinement stepCycle: final / Resolution: 1.526→44.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 68 405 3494
Biso mean--14.38 31.22 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093194
X-RAY DIFFRACTIONf_angle_d1.0844368
X-RAY DIFFRACTIONf_chiral_restr0.059473
X-RAY DIFFRACTIONf_plane_restr0.008582
X-RAY DIFFRACTIONf_dihedral_angle_d18.1871909
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.526-1.56370.31621340.2969338091
1.5637-1.60590.32291420.2604359597
1.6059-1.65320.23191490.2405360597
1.6532-1.70660.2881340.2282362997
1.7066-1.76760.22711490.2047359997
1.7676-1.83830.20091410.1788365298
1.8383-1.9220.18261360.1565362598
1.922-2.02330.19541470.1558368698
2.0233-2.15010.2181380.1485363798
2.1501-2.31610.17621410.1471369799
2.3161-2.54910.20041460.155371799
2.5491-2.91790.21621380.1646371899
2.9179-3.6760.17351470.15373771100
3.676-44.4820.16531480.14653827100

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