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- PDB-7kcs: The crystal structure of 4-vinylbenzoate-bound wild-type CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 7kcs
TitleThe crystal structure of 4-vinylbenzoate-bound wild-type 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: 1.773 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
DepositionOct 7, 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)45,3884
Polymers44,5871
Non-polymers8003
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-37 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.312, 51.387, 79.008
Angle α, β, γ (deg.)90.000, 92.160, 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 (E. coli) / References: UniProt: Q2IU02, Oxidoreductases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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-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


Mass: 18.015 Da / Num. of mol.: 329 / 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: 41.3 % / Description: flat plates
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 1 mM substrate, 0.2 M magnesium acetate tetrahydrate, 20-23% w/v PEG3350, 0.1 M Bis-Tris, pH 5.25, 500 uL reservoir, crystals grew in 2 weeks
PH range: 5.25-6 / Temp details: 16 C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→43.07 Å / Num. obs: 34471 / % possible obs: 99.4 % / Redundancy: 7.3 % / Biso Wilson estimate: 15.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.048 / Rrim(I) all: 0.129 / Net I/σ(I): 10.4 / Num. measured all: 251037 / Scaling rejects: 3
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
1.77-1.816.80.831220117950.7590.3350.8971.893
9.04-43.076.50.0418562860.9960.0170.04434.399

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.75 Å39.48 Å
Translation5.75 Å39.48 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.25data scaling
PHASER2.7.17phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4DO1

4do1


Resolution: 1.773→39.476 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1776 5.15 %Randomly selected
Rwork0.1948 32678 --
obs0.197 34454 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.41 Å2 / Biso mean: 17.4862 Å2 / Biso min: 5.46 Å2
Refinement stepCycle: final / Resolution: 1.773→39.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 55 329 3405
Biso mean--11.95 24.95 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063192
X-RAY DIFFRACTIONf_angle_d0.8524366
X-RAY DIFFRACTIONf_chiral_restr0.049473
X-RAY DIFFRACTIONf_plane_restr0.006582
X-RAY DIFFRACTIONf_dihedral_angle_d8.7172617
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7733-1.82130.32421380.2629238796
1.8213-1.87490.29621160.243250399
1.8749-1.93540.29391560.22192518100
1.9354-2.00450.29131200.21162500100
2.0045-2.08480.25011330.20562497100
2.0848-2.17970.2621380.2012495100
2.1797-2.29460.23411180.1952545100
2.2946-2.43830.23861720.20282501100
2.4383-2.62660.23521190.20932534100
2.6266-2.89080.26241380.21092511100
2.8908-3.30890.22991510.20482527100
3.3089-4.16820.20191390.16372549100
4.1682-39.4760.19031380.15842611100

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