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- PDB-8gm2: Crystal structure of T252E-CYP199A4 in complex with 4-methoxybenz... -

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Basic information

Entry
Database: PDB / ID: 8gm2
TitleCrystal structure of T252E-CYP199A4 in complex with 4-methoxybenzoic acid soaked with 2 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
4-METHOXYBENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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 24, 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)45,3703
Polymers44,6011
Non-polymers7692
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.372, 51.640, 79.055
Angle α, β, γ (deg.)90.00, 92.31, 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-ANN / 4-METHOXYBENZOIC ACID / P-ANISIC ACID


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.33→44.34 Å / Num. obs: 15455 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.058 / Rrim(I) all: 0.148 / Χ2: 0.95 / Net I/σ(I): 11.9 / Num. measured all: 99887
Reflection shellResolution: 2.33→2.41 Å / % possible obs: 99.6 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.814 / Num. measured all: 9512 / Num. unique obs: 1489 / CC1/2: 0.893 / Rpim(I) all: 0.35 / Rrim(I) all: 0.888 / Χ2: 0.98 / Net I/σ(I) obs: 3

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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: 2.33→44.34 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 31.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 1530 9.93 %
Rwork0.2083 --
obs0.2142 15402 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 54 73 3150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033167
X-RAY DIFFRACTIONf_angle_d0.6154327
X-RAY DIFFRACTIONf_dihedral_angle_d20.748445
X-RAY DIFFRACTIONf_chiral_restr0.043469
X-RAY DIFFRACTIONf_plane_restr0.004575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.410.39991360.31811238X-RAY DIFFRACTION99
2.41-2.490.36211340.31671244X-RAY DIFFRACTION99
2.49-2.590.40261370.29571262X-RAY DIFFRACTION99
2.59-2.710.32871400.27591250X-RAY DIFFRACTION99
2.71-2.850.34251350.26461246X-RAY DIFFRACTION100
2.85-3.030.29831480.24691267X-RAY DIFFRACTION100
3.03-3.260.29151370.22421233X-RAY DIFFRACTION100
3.26-3.590.24791380.19261270X-RAY DIFFRACTION100
3.59-4.110.221380.16521276X-RAY DIFFRACTION100
4.11-5.180.20921410.15781273X-RAY DIFFRACTION99
5.18-44.340.2391460.17631313X-RAY DIFFRACTION100

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