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- PDB-8taw: The crystal structure of T252E CYP199A4 bound to 4-(pyridin-2-yl)... -

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Basic information

Entry
Database: PDB / ID: 8taw
TitleThe crystal structure of T252E CYP199A4 bound to 4-(pyridin-2-yl)benzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / peroxygenase mutant / inhibitor
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-(pyridin-2-yl)benzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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: Characterisation of the heme aqua-ligand coordination environment in an engineered peroxygenase cytochrome P450 variant.
Authors: Podgorski, M.N. / Lee, J.H.Z. / Harbort, J.S. / Nguyen, G.T.H. / Doherty, D.Z. / Donald, W.A. / Harmer, J.R. / Bruning, J.B. / Bell, S.G.
History
DepositionJun 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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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)45,4674
Polymers44,6151
Non-polymers8513
Water10,413578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.170, 51.520, 79.230
Angle α, β, γ (deg.)90.00, 92.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 44615.438 Da / Num. of mol.: 1 / Mutation: T252E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic)
Gene: RPB_3613 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2IU02
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#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-PQS / 4-(pyridin-2-yl)benzoic acid


Mass: 199.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.02 Å3/Da / Density % sol: 39.08 %
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: 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: 1.73→44.134 Å / Num. obs: 37249 / % possible obs: 99.7 % / Redundancy: 7.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.052 / Rrim(I) all: 0.14 / Χ2: 0.94 / Net I/σ(I): 13.1
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 94.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.875 / Num. measured all: 12999 / Num. unique obs: 1933 / CC1/2: 0.7 / Rpim(I) all: 0.361 / Rrim(I) all: 0.949 / Χ2: 0.74 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→44.134 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1848 1893 5.08 %
Rwork0.1517 --
obs0.1533 37232 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→44.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 59 578 3660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063217
X-RAY DIFFRACTIONf_angle_d0.8254397
X-RAY DIFFRACTIONf_dihedral_angle_d24.4851188
X-RAY DIFFRACTIONf_chiral_restr0.046476
X-RAY DIFFRACTIONf_plane_restr0.005585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.77330.26081330.22392408X-RAY DIFFRACTION96
1.7733-1.82120.23921480.2012488X-RAY DIFFRACTION100
1.8212-1.87480.25821510.18932485X-RAY DIFFRACTION100
1.8748-1.93530.19881480.18442541X-RAY DIFFRACTION100
1.9353-2.00450.19131600.17212478X-RAY DIFFRACTION100
2.0045-2.08470.18291390.15212497X-RAY DIFFRACTION100
2.0847-2.17960.21221180.14832521X-RAY DIFFRACTION100
2.1796-2.29450.1771030.14622575X-RAY DIFFRACTION100
2.2945-2.43830.17581370.14692539X-RAY DIFFRACTION100
2.4383-2.62650.18311540.14972509X-RAY DIFFRACTION100
2.6265-2.89080.18521180.15522537X-RAY DIFFRACTION100
2.8908-3.3090.17551380.14292547X-RAY DIFFRACTION100
3.309-4.16850.16311200.12272577X-RAY DIFFRACTION100
4.1685-44.1340.14821260.14172637X-RAY DIFFRACTION100

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