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- PDB-8vkf: The crystal structure of wild-type CYP199A4 bound to 4-propionylb... -

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Basic information

Entry
Database: PDB / ID: 8vkf
TitleThe crystal structure of wild-type CYP199A4 bound to 4-propionylbenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / CYP199A4
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: 1.7 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 9, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4425
Polymers44,5871
Non-polymers8544
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.954, 51.322, 79.119
Angle α, β, γ (deg.)90.00, 92.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 458 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-LVK / 4-propanoylbenzoic acid


Mass: 178.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.86 Å3/Da / Density % sol: 33.98 %
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: 1.7→43.04 Å / Num. obs: 36229 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.074 / Rrim(I) all: 0.189 / Χ2: 0.95 / Net I/σ(I): 7.4 / Num. measured all: 234344
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 1.638 / Num. measured all: 12545 / Num. unique obs: 1906 / CC1/2: 0.67 / Rpim(I) all: 0.689 / Rrim(I) all: 1.781 / Χ2: 0.76 / Net I/σ(I) obs: 1.6

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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: 1.7→40.913 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 1866 5.16 %
Rwork0.1755 --
obs0.1773 36180 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→40.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 58 454 3533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043185
X-RAY DIFFRACTIONf_angle_d0.7064353
X-RAY DIFFRACTIONf_dihedral_angle_d23.421173
X-RAY DIFFRACTIONf_chiral_restr0.044472
X-RAY DIFFRACTIONf_plane_restr0.005580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7460.30171580.25672595X-RAY DIFFRACTION100
1.746-1.79740.31971180.24832644X-RAY DIFFRACTION100
1.7974-1.85540.28481530.23222622X-RAY DIFFRACTION100
1.8554-1.92170.26821280.21752620X-RAY DIFFRACTION100
1.9217-1.99860.26361660.21082587X-RAY DIFFRACTION100
1.9986-2.08960.24471740.19532603X-RAY DIFFRACTION100
2.0896-2.19970.26061470.18472652X-RAY DIFFRACTION100
2.1997-2.33760.22031390.17412632X-RAY DIFFRACTION100
2.3376-2.5180.22191230.17212651X-RAY DIFFRACTION100
2.518-2.77140.20321250.17212670X-RAY DIFFRACTION100
2.7714-3.17230.21611530.17282656X-RAY DIFFRACTION100
3.1723-3.99620.14931250.14612658X-RAY DIFFRACTION99
3.9962-40.9130.16081570.14632724X-RAY DIFFRACTION100

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