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- PDB-8vl0: The crystal structure of wild-type CYP199A4 bound to 4-(2-oxoprop... -

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Basic information

Entry
Database: PDB / ID: 8vl0
TitleThe crystal structure of wild-type CYP199A4 bound to 4-(2-oxopropyl)benzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome P450 / 4-(2-oxopropyl)benzoic 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 / : / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.837 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Acs Catalysis / Year: 2024
Title: Selective alpha -Hydroxyketone Formation and Subsequent C-C Bond Cleavage by Cytochrome P450 Monooxygenase Enzymes.
Authors: Lee, J.H.Z. / Coleman, T. / Mclean, M.A. / Podgorski, M.N. / Hayball, E.F. / Stone, I.S.J. / Bruning, J.B. / Whelan, F. / Voss, J.J. / Sligar, S.G. / Bell, S.G.
History
DepositionJan 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: 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 1.2Feb 19, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_entry_details.has_protein_modification

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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)45,4184
Polymers44,5871
Non-polymers8303
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.179, 51.407, 79.296
Angle α, β, γ (deg.)90.00, 92.01, 90.00
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 HaA2 (phototrophic)
Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02
#2: Chemical ChemComp-LVC / 4-(2-oxopropyl)benzoic acid


Mass: 178.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O3 / 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.: 398 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.88 Å3/Da / Density % sol: 34.62 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: The crystallization buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate and 20-32% PEG 3350
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: MX1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 12, 2020
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.83→43.13 Å / Num. obs: 29073 / % possible obs: 98.8 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.068 / Rrim(I) all: 0.176 / Χ2: 0.54 / Net I/σ(I): 7 / Num. measured all: 190714
Reflection shellResolution: 1.83→1.87 Å / % possible obs: 83.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.911 / Num. measured all: 8639 / Num. unique obs: 1497 / CC1/2: 0.351 / Rpim(I) all: 0.857 / Rrim(I) all: 2.102 / Χ2: 0.45 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.837→43.128 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 1996 6.9 %
Rwork0.1828 --
obs0.1855 28934 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.837→43.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 57 398 3476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023192
X-RAY DIFFRACTIONf_angle_d0.5874364
X-RAY DIFFRACTIONf_dihedral_angle_d21.4441178
X-RAY DIFFRACTIONf_chiral_restr0.04473
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.837-1.88260.37291410.33981828X-RAY DIFFRACTION94
1.8826-1.93350.32281360.29431909X-RAY DIFFRACTION99
1.9335-1.99040.30851360.26011914X-RAY DIFFRACTION99
1.9904-2.05460.27921490.22691943X-RAY DIFFRACTION100
2.0546-2.12810.26451290.21491900X-RAY DIFFRACTION100
2.1281-2.21330.23221490.20391919X-RAY DIFFRACTION100
2.2133-2.3140.24641460.20411906X-RAY DIFFRACTION100
2.314-2.4360.26111450.19311938X-RAY DIFFRACTION100
2.436-2.58860.24141440.17771919X-RAY DIFFRACTION100
2.5886-2.78840.22451380.18091926X-RAY DIFFRACTION100
2.7884-3.06890.22851420.17191939X-RAY DIFFRACTION100
3.0689-3.51290.19021410.15111946X-RAY DIFFRACTION100
3.5129-4.42510.15021490.14081954X-RAY DIFFRACTION100
4.4251-43.1280.19411510.1591997X-RAY DIFFRACTION100

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