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- PDB-6pqw: The crystal structure of 3-methylbenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6pqw
TitleThe crystal structure of 3-methylbenzoate-bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / 3-methylbenzoic 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 / 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
PROTOPORPHYRIN IX CONTAINING FE / 3-methylbenzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.679 Å
AuthorsPodgorski, M.N. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 and ANSTO Australian Synchrotron Collaborative Access Program (CAP) grant MXCAP12393/13630 Australia
CitationJournal: J.Inorg.Biochem. / Year: 2019
Title: Investigation of the requirements for efficient and selective cytochrome P450 monooxygenase catalysis across different reactions.
Authors: Podgorski, M.N. / Coleman, T. / Chao, R.R. / De Voss, J.J. / Bruning, J.B. / Bell, S.G.
History
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3764
Polymers44,5871
Non-polymers7883
Water8,935496
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-37 kcal/mol
Surface area14920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.449, 51.235, 78.955
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 BL21(DE3) (bacteria) / References: UniProt: Q2IU02
#2: Chemical ChemComp-OVV / 3-methylbenzoic acid


Mass: 136.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M magnesium acetate, 100 mM Bis-Tris adjusted with acetic acid to pH 5.0-5.75, 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: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 14, 2018
RadiationMonochromator: double-crystal Si(111) liquid nitrogen cooled (DC) or channel-cut Si(111) liquid nitrogen cooled (CC)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.679→44.42 Å / Num. obs: 40638 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 14.3
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
1.68-1.716.90.5681413220580.9150.2310.6142.697.3
9.04-44.426.50.02918622860.9990.0120.03147.299.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.83 Å42.97 Å
Translation5.83 Å42.97 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVB

5uvb


Resolution: 1.679→42.97 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.44
RfactorNum. reflection% reflection
Rfree0.1879 2000 4.92 %
Rwork0.1444 --
obs0.1466 40615 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.99 Å2 / Biso mean: 18.4522 Å2 / Biso min: 7.71 Å2
Refinement stepCycle: final / Resolution: 1.679→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 54 496 3571
Biso mean--12.17 29.01 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133187
X-RAY DIFFRACTIONf_angle_d1.0354357
X-RAY DIFFRACTIONf_chiral_restr0.059473
X-RAY DIFFRACTIONf_plane_restr0.007580
X-RAY DIFFRACTIONf_dihedral_angle_d10.5382616
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6794-1.72140.26361450.2137268798
1.7214-1.7680.20171450.17532756100
1.768-1.820.17681430.15972713100
1.82-1.87880.21981380.15662765100
1.8788-1.94590.20221440.15642732100
1.9459-2.02380.21021420.15562757100
2.0238-2.11590.21081440.13822756100
2.1159-2.22750.18081410.14372756100
2.2275-2.3670.18451370.14042741100
2.367-2.54980.20441510.15272774100
2.5498-2.80630.20461370.162769100
2.8063-3.21230.20821430.14862770100
3.2123-4.04670.15541420.12282794100
4.0467-42.970.1531480.12642845100

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