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- PDB-8tay: The crystal structure of T252E CYP199A4 bound to 4-(thiophen-3-yl... -

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Basic information

Entry
Database: PDB / ID: 8tay
TitleThe crystal structure of T252E CYP199A4 bound to 4-(thiophen-3-yl)benzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / peroxygenase
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
4-(thiophen-3-yl)benzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.021 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)45,4724
Polymers44,6151
Non-polymers8563
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.120, 51.574, 79.530
Angle α, β, γ (deg.)90.00, 92.39, 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-EJD / 4-(thiophen-3-yl)benzoic acid


Mass: 204.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O2S / 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.: 362 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
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: 0.95373 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: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.02→44.082 Å / Num. obs: 23380 / % possible obs: 98.8 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.054 / Rrim(I) all: 0.141 / Χ2: 0.53 / Net I/σ(I): 8.1
Reflection shellResolution: 2.02→2.07 Å / % possible obs: 89.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.632 / Num. measured all: 8947 / Num. unique obs: 1558 / CC1/2: 0.874 / Rpim(I) all: 0.281 / Rrim(I) all: 0.694 / Χ2: 0.51 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5uvb

5uvb


Resolution: 2.021→44.082 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2226 1986 8.51 %
Rwork0.1765 --
obs0.1805 23333 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.021→44.082 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 58 362 3443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063188
X-RAY DIFFRACTIONf_angle_d0.6724353
X-RAY DIFFRACTIONf_dihedral_angle_d8.7582611
X-RAY DIFFRACTIONf_chiral_restr0.043469
X-RAY DIFFRACTIONf_plane_restr0.005579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.021-2.07110.2911250.23371388X-RAY DIFFRACTION90
2.0711-2.12710.25511490.21021520X-RAY DIFFRACTION99
2.1271-2.18970.27191440.20351528X-RAY DIFFRACTION99
2.1897-2.26040.25261380.19941510X-RAY DIFFRACTION99
2.2604-2.34120.27391330.18131547X-RAY DIFFRACTION99
2.3412-2.43490.28621430.19171521X-RAY DIFFRACTION100
2.4349-2.54570.25381400.19141513X-RAY DIFFRACTION99
2.5457-2.67990.2381460.18981511X-RAY DIFFRACTION99
2.6799-2.84780.25321370.1931538X-RAY DIFFRACTION99
2.8478-3.06760.27081420.18261538X-RAY DIFFRACTION99
3.0676-3.37620.20071450.17431536X-RAY DIFFRACTION99
3.3762-3.86450.19521460.15921537X-RAY DIFFRACTION100
3.8645-4.86790.19721470.14251567X-RAY DIFFRACTION100
4.8679-44.0820.15251510.15991593X-RAY DIFFRACTION100

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