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- PDB-6wzp: The crystal structure of 4-vinylbenzoate-bound T252A mutant CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6wzp
TitleThe crystal structure of 4-vinylbenzoate-bound T252A mutant CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450 / Substrate
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-ethenylbenzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsColeman, T. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: Acs Catalysis / Year: 2021
Title: Understanding the Mechanistic Requirements for Efficient and Stereoselective Alkene Epoxidation by a Cytochrome P450 Enzyme
Authors: Coleman, T. / Kirk, A.M. / Chao, R.R. / Podgorski, M.N. / Harbort, J.S. / Churchman, L.R. / Bruning, J.B. / Bernhardt, P.V. / Harmer, J.R. / Krenske, E.H. / De Voss, J.J. / Bell, S.G.
History
DepositionMay 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,6694
Polymers42,8691
Non-polymers8003
Water13,043724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-37 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.060, 51.050, 78.480
Angle α, β, γ (deg.)90.000, 92.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / / CYP199A4


Mass: 42868.633 Da / Num. of mol.: 1 / Mutation: T252A
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 (E. coli) / References: UniProt: Q2IU02
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-MW7 / 4-ethenylbenzoic acid


Mass: 148.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 724 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M magnesium acetate, 23% w/v PEG3350, 0.1 M Bis-Tris, pH 5.5
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: Mar 15, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→39.21 Å / Num. obs: 41516 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 8.95 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.081 / Rrim(I) all: 0.205 / Net I/σ(I): 7.5 / Num. measured all: 256584 / Scaling rejects: 226
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
1.65-1.685.90.4381202720390.8390.1880.4793.699.2
9.04-39.2160.12313582270.9810.0530.13510.287.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.68 Å33.33 Å
Translation5.68 Å33.33 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DO1

4do1


Resolution: 1.65→33.331 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2124 5.12 %Random selection
Rwork0.2011 39383 --
obs0.2037 41507 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 34.89 Å2 / Biso mean: 11.6813 Å2 / Biso min: 2.65 Å2
Refinement stepCycle: final / Resolution: 1.65→33.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 55 724 3798
Biso mean--5.02 18.27 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043193
X-RAY DIFFRACTIONf_angle_d0.7484366
X-RAY DIFFRACTIONf_chiral_restr0.043472
X-RAY DIFFRACTIONf_plane_restr0.005582
X-RAY DIFFRACTIONf_dihedral_angle_d8.6982615
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.68840.3491360.2708262199
1.6884-1.73060.32991270.2554261898
1.7306-1.77740.32441350.251260198
1.7774-1.82970.2521460.2469260398
1.8297-1.88870.27961460.2414258199
1.8887-1.95620.26041380.2397265299
1.9562-2.03460.26941250.2216263199
2.0346-2.12710.28831430.2125261099
2.1271-2.23930.25461370.2099264699
2.2393-2.37950.23981640.2033261299
2.3795-2.56320.25671550.201263799
2.5632-2.8210.25611460.2017263799
2.821-3.22890.23261560.1831263799
3.2289-4.0670.20991410.1545266399
4.067-33.3310.18681290.1497263495

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