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- PDB-6pqd: The crystal structure of 3-methylthiobenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6pqd
TitleThe crystal structure of 3-methylthiobenzoate-bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / 3-methylthiobenzoic 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-(methylsulfanyl)benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsPodgorski, M.N. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) 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 9, 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)45,4084
Polymers44,5871
Non-polymers8203
Water8,125451
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-37 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.290, 51.270, 78.740
Angle α, β, γ (deg.)90.000, 92.550, 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OVP / 3-(methylsulfanyl)benzoic acid


Mass: 168.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2S / 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.: 451 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1:1 35-40 mg/mL CYP199A4 (in 50 mM Tris-HCl, pH 7.4) + reservoir (0.2 M magnesium acetate, 100 mM Bis-Tris buffer 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: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 18, 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: 1.89→44.25 Å / Num. obs: 28336 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 14.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.042 / Rrim(I) all: 0.111 / Net I/σ(I): 13.6 / Num. measured all: 188829 / Scaling rejects: 19
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
1.89-1.936.10.4621066517500.9020.2020.505495.1
9.06-44.255.90.05316922870.9950.0230.0582999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.8 Å44.25 Å
Translation5.8 Å44.25 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.6.2data scaling
PHASER2.7.17phasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVB

5uvb


Resolution: 1.89→44.246 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.67
RfactorNum. reflection% reflection
Rfree0.2 1450 5.12 %
Rwork0.154 --
obs0.1564 28315 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.41 Å2 / Biso mean: 17.2464 Å2 / Biso min: 4.26 Å2
Refinement stepCycle: final / Resolution: 1.89→44.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 55 451 3527
Biso mean--10.95 25.3 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073204
X-RAY DIFFRACTIONf_angle_d0.8434382
X-RAY DIFFRACTIONf_chiral_restr0.048475
X-RAY DIFFRACTIONf_plane_restr0.006585
X-RAY DIFFRACTIONf_dihedral_angle_d8.4982621
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.89-1.95760.26551550.1993257697
1.9576-2.0360.21761470.17792671100
2.036-2.12860.22421250.16762697100
2.1286-2.24080.25091310.16232695100
2.2408-2.38120.22341440.15082658100
2.3812-2.56510.19851240.157270699
2.5651-2.82320.21861580.16172680100
2.8232-3.23160.19741420.15762712100
3.2316-4.0710.16711690.13432695100
4.071-44.2460.17171550.13962775100

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