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- PDB-7trt: The crystal structure of CYP199A4 bound to 4-(furan-2-yl)benzoic acid -

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Basic information

Entry
Database: PDB / ID: 7trt
TitleThe crystal structure of CYP199A4 bound to 4-(furan-2-yl)benzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / heterocycle / furan
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-(furan-2-yl)benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.42 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Chemistry / Year: 2023
Title: The Oxidation of Oxygen and Sulfur-Containing Heterocycles by Cytochrome P450 Enzymes.
Authors: Podgorski, M.N. / Keto, A.B. / Coleman, T. / Bruning, J.B. / De Voss, J.J. / Krenske, E.H. / Bell, S.G.
History
DepositionJan 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)45,4525
Polymers44,5871
Non-polymers8644
Water11,548641
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.205, 51.449, 79.454
Angle α, β, γ (deg.)90.000, 92.120, 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 / CYP199A4


Mass: 44587.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02

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Non-polymers , 5 types, 645 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#3: Chemical ChemComp-KQF / 4-(furan-2-yl)benzoic acid


Mass: 188.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O3 / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.02 Å3/Da / Density % sol: 39.26 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: The crystallisation buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic acid), 0.2 M magnesium acetate and 20-32% PEG 3350
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: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2020
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: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.42→44.175 Å / Num. obs: 67228 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 11.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Rrim(I) all: 0.07 / 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
1.42-1.446.70.472148432270.920.1970.511397.4
7.78-44.176.50.03529064470.9980.0150.03842.599.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.84 Å44.17 Å
Translation5.84 Å44.17 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UVB

5uvb


Resolution: 1.42→44.175 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1718 2007 2.99 %
Rwork0.1489 65191 -
obs0.1495 67198 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.6 Å2 / Biso mean: 16.6933 Å2 / Biso min: 6.24 Å2
Refinement stepCycle: final / Resolution: 1.42→44.175 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 66 649 3736
Biso mean--9.85 29.15 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123280
X-RAY DIFFRACTIONf_angle_d1.2324501
X-RAY DIFFRACTIONf_chiral_restr0.097487
X-RAY DIFFRACTIONf_plane_restr0.01605
X-RAY DIFFRACTIONf_dihedral_angle_d23.5241211
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4204-1.4560.24781410.2005451098
1.456-1.49530.2541440.19134647100
1.4953-1.53930.23391390.17914632100
1.5393-1.5890.21641370.17714648100
1.589-1.64580.18941440.17314631100
1.6458-1.71170.22951460.16474648100
1.7117-1.78960.16641440.15584650100
1.7896-1.8840.17971410.14974649100
1.884-2.0020.15261460.14714669100
2.002-2.15660.15721410.14584654100
2.1566-2.37360.16151410.14044650100
2.3736-2.7170.18151480.14724720100
2.717-3.4230.16831420.14174700100
3.423-44.1750.14041530.1324783100

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