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- PDB-6u31: The crystal structure of 4-(1H-imidazol-1-yl)benzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6u31
TitleThe crystal structure of 4-(1H-imidazol-1-yl)benzoate-bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / 4-(1H-imidazol-1-yl)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 / 4-(1H-imidazol-1-yl)benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.578 Å
AuthorsPodgorski, M.N. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: Inorg.Chem. / Year: 2022
Title: To Be, or Not to Be, an Inhibitor: A Comparison of Azole Interactions with and Oxidation by a Cytochrome P450 Enzyme.
Authors: Podgorski, M.N. / Coleman, T. / Giang, P.D. / Wang, C.R. / Bruning, J.B. / Bernhardt, P.V. / De Voss, J.J. / Bell, S.G.
History
DepositionAug 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4284
Polymers44,5871
Non-polymers8403
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-36 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.420, 51.420, 78.850
Angle α, β, γ (deg.)90.000, 92.310, 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; Acting on paired donors, with incorporation or reduction of molecular oxygen
#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-PQP / 4-(1H-imidazol-1-yl)benzoic acid


Mass: 188.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2O2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M magnesium acetate, 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 29, 2018
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.578→44.38 Å / Num. obs: 48847 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 11.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Net I/σ(I): 18.2
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
1.58-1.66.50.571551723880.870.240.623.399
8.64-44.386.20.02319683200.9990.010.02549.598.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.84 Å43.06 Å
Translation5.84 Å43.06 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.6.3data scaling
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVB

5uvb


Resolution: 1.578→43.06 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.56
RfactorNum. reflection% reflection
Rfree0.1782 2461 5.04 %
Rwork0.1449 --
obs0.1466 48827 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.31 Å2 / Biso mean: 14.4842 Å2 / Biso min: 4.44 Å2
Refinement stepCycle: final / Resolution: 1.578→43.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 58 628 3707
Biso mean--9.15 25.71 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073301
X-RAY DIFFRACTIONf_angle_d0.9424528
X-RAY DIFFRACTIONf_chiral_restr0.054488
X-RAY DIFFRACTIONf_plane_restr0.006609
X-RAY DIFFRACTIONf_dihedral_angle_d8.8373349
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.578-1.60840.25981300.189252099
1.6084-1.64120.22771470.18282567100
1.6412-1.67690.23551300.18272554100
1.6769-1.71590.22081300.17822586100
1.7159-1.75880.23991410.1732527100
1.7588-1.80640.19171670.15942556100
1.8064-1.85950.2161500.1581252899
1.8595-1.91950.20411330.1524257399
1.9195-1.98810.17911420.1495256899
1.9881-2.06770.21171320.1504256199
2.0677-2.16180.17511340.1388255399
2.1618-2.27580.15251350.1367256399
2.2758-2.41840.19031250.1383259299
2.4184-2.60510.18311140.14362625100
2.6051-2.86720.17411170.14682617100
2.8672-3.2820.15071660.14122567100
3.282-4.13440.1411230.12182631100
4.1344-43.060.15461450.13092678100

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