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- PDB-8glz: Crystal structure of T252E-CYP199A4 in complex with 4-hydroxybenz... -

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Basic information

Entry
Database: PDB / ID: 8glz
TitleCrystal structure of T252E-CYP199A4 in complex with 4-hydroxybenzoic acid. Crystal was initially co-crystallised with 4-methoxybenzoic acid and soaked with 4 mM hydrogen peroxide
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / cytochrome / bacterial P450
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 / P-HYDROXYBENZOIC ACID / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsLee, J.H.Z. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: Chemistry / Year: 2024
Title: An In Crystallo Reaction with an Engineered Cytochrome P450 Peroxygenase.
Authors: Lee, J.H.Z. / Bruning, J.B. / Bell, S.G.
History
DepositionMar 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year

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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)45,3914
Polymers44,6011
Non-polymers7903
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.168, 51.615, 79.456
Angle α, β, γ (deg.)90.00, 92.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 44601.410 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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / 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.: 234 / 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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M magnesium acetate, 100 mM Bis-Tris buffer (adjusted with acetic acid to pH 5.0-5.75) 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: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.02→41.14 Å / Num. obs: 21694 / % possible obs: 0.963 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Net I/σ(I): 0.174
Reflection shellResolution: 2.02→2.07 Å / Rmerge(I) obs: 0.885 / Num. unique obs: 1563 / CC1/2: 0.907

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→41.14 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 1992 9.2 %
Rwork0.1952 --
obs0.2 21644 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 54 234 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083166
X-RAY DIFFRACTIONf_angle_d0.984326
X-RAY DIFFRACTIONf_dihedral_angle_d20.874444
X-RAY DIFFRACTIONf_chiral_restr0.052469
X-RAY DIFFRACTIONf_plane_restr0.006575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.070.3971370.34431371X-RAY DIFFRACTION96
2.07-2.130.33241460.27381367X-RAY DIFFRACTION98
2.13-2.190.32041330.21441408X-RAY DIFFRACTION98
2.19-2.260.26181490.19741377X-RAY DIFFRACTION97
2.26-2.340.28071370.19591376X-RAY DIFFRACTION98
2.34-2.430.24591420.19561434X-RAY DIFFRACTION99
2.43-2.540.23991400.18851390X-RAY DIFFRACTION98
2.55-2.680.27191330.19521386X-RAY DIFFRACTION97
2.68-2.850.23291480.20791396X-RAY DIFFRACTION98
2.85-3.070.26251430.21361404X-RAY DIFFRACTION99
3.07-3.370.25261400.20031427X-RAY DIFFRACTION99
3.38-3.860.23041470.18511421X-RAY DIFFRACTION98
3.86-4.870.20411440.16561421X-RAY DIFFRACTION99
4.87-41.140.2211530.17181474X-RAY DIFFRACTION99

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