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- PDB-7u00: The crystal structure of WT CYP199A4 bound to 4-(2-chloroethyl)be... -

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Basic information

Entry
Database: PDB / ID: 7u00
TitleThe crystal structure of WT CYP199A4 bound to 4-(2-chloroethyl)benzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / 4-(2-chloroethyl)benzoic 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, 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-(2-chloroethyl)benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.657 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Cytochrome P450-catalyzed oxidation of halogen-containing substrates.
Authors: Coleman, T. / Podgorski, M.N. / Doyle, M.L. / Scaffidi-Muta, J.M. / Campbell, E.C. / Bruning, J.B. / De Voss, J.J. / Bell, S.G.
History
DepositionFeb 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 10, 2023Group: 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 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)45,4485
Polymers44,5871
Non-polymers8614
Water12,178676
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.137, 51.430, 79.334
Angle α, β, γ (deg.)90.000, 91.980, 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, 680 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-L4I / 4-(2-chloroethyl)benzoic acid


Mass: 184.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9ClO2 / 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.: 676 / 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: 39.06 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: For crystallisation, CYP199A4 was concentrated to approx. 40 mg mL-1 in 50 mM Tris buffer, pH 7.4. The crystallisation buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with acetic ...Details: For crystallisation, CYP199A4 was concentrated to approx. 40 mg mL-1 in 50 mM Tris buffer, pH 7.4. 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: 5.00-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2021
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: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.657→44.11 Å / Num. obs: 42157 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.989 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.104 / Rrim(I) all: 0.276 / Net I/σ(I): 4.8
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
1.66-1.686.31.6841123617960.3930.7021.8290.886.8
9.07-44.116.20.05917422830.9960.0250.06419.399

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.83 Å43.15 Å
Translation5.83 Å43.15 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: 1.657→43.148 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 1999 4.75 %
Rwork0.1668 40120 -
obs0.1683 42119 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.12 Å2 / Biso mean: 15.7698 Å2 / Biso min: 5.74 Å2
Refinement stepCycle: final / Resolution: 1.657→43.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 85 679 3785
Biso mean--10.6 25.67 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023203
X-RAY DIFFRACTIONf_angle_d0.6354379
X-RAY DIFFRACTIONf_chiral_restr0.04474
X-RAY DIFFRACTIONf_plane_restr0.003583
X-RAY DIFFRACTIONf_dihedral_angle_d18.2441913
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.657-1.69840.27761260.2756259391
1.6984-1.74430.29631410.25642861100
1.7443-1.79560.25731380.23352868100
1.7956-1.85360.26541530.22382871100
1.8536-1.91980.24561470.20942873100
1.9198-1.99670.23971340.19642885100
1.9967-2.08760.20121450.18462863100
2.0876-2.19760.19381430.16172899100
2.1976-2.33530.17711450.15242861100
2.3353-2.51560.18511430.15482869100
2.5156-2.76870.19651420.15732900100
2.7687-3.16930.17641470.1512902100
3.1693-3.99250.17891440.12672911100
3.9925-43.1480.16781510.13862964100

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