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- PDB-5kt1: The crystal structure of 4-methylthiobenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 5kt1
TitleThe crystal structure of 4-methylthiobenzoate-bound 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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-methylsulfanylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.015 Å
AuthorsColeman, T. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: To Be Published
Title: The crystal structure of 4-methylthiobenzoate-bound CYP199A4
Authors: Coleman, T. / Bruning, J.B. / Bell, S.G.
History
DepositionJul 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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)43,8115
Polymers42,8991
Non-polymers9124
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.069, 51.279, 78.983
Angle α, β, γ (deg.)90.000, 91.820, 90.000
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


Mass: 42898.660 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

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Non-polymers , 5 types, 370 molecules

#2: Chemical ChemComp-4MI / 4-methylsulfanylbenzoic acid


Mass: 168.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2S
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.84 %
Description: rectangular plate - approx dimensions 300 um by 150 um by 20 um
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Magnesium acetate PEG 3350 - 23% w/v Bis-Tris 0.1M - pH 5.5
PH range: 5.25-6 / Temp details: 16 celsius

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.01→44.05 Å / Num. obs: 23479 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.984 / Rmerge(I) obs: 0.297 / Rpim(I) all: 0.119 / Rrim(I) all: 0.32 / Net I/σ(I): 7.2 / Num. measured all: 167452 / Scaling rejects: 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.01-2.076.70.8940.828197.2
9.01-44.056.70.0510.998199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.01 Å44.05 Å
Translation2.01 Å44.05 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.25data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 4DO1

4do1


Resolution: 2.015→44.047 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 1221 5.21 %Random selection.
Rwork0.1555 ---
obs0.159 23456 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.7 Å2 / Biso mean: 18.5446 Å2 / Biso min: 4.88 Å2
Refinement stepCycle: final / Resolution: 2.015→44.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 61 366 3448
Biso mean--15.54 25.79 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123167
X-RAY DIFFRACTIONf_angle_d1.3774326
X-RAY DIFFRACTIONf_chiral_restr0.048470
X-RAY DIFFRACTIONf_plane_restr0.007573
X-RAY DIFFRACTIONf_dihedral_angle_d14.1081165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0147-2.09540.31251240.23262421254598
2.0954-2.19070.33711460.209124672613100
2.1907-2.30620.28611530.185524062559100
2.3062-2.45070.23141470.17824542601100
2.4507-2.63990.23651440.164424462590100
2.6399-2.90550.23251340.161424752609100
2.9055-3.32580.241360.144524742610100
3.3258-4.18970.15851100.116725142624100
4.1897-44.05740.14441270.125825782705100

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