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- PDB-8vfr: The crystal structure of 4-methylbenzoic acid-bound GALQE CYP199A... -

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Basic information

Entry
Database: PDB / ID: 8vfr
TitleThe crystal structure of 4-methylbenzoic acid-bound GALQE CYP199A4 after soaking in 10 mM H2O2 for 5 minutes
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 enzyme / 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-METHYLBENZOIC ACID / 4-(hydroxymethyl)benzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.018 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Acs Catalysis / Year: 2024
Title: Engineering Peroxygenase Activity into Cytochrome P450 Monooxygenases through Modification of the Oxygen Binding Region
Authors: Podgorski, M.N. / Akter, J. / Churchman, L.R. / Bruning, J.B. / De Voss, J.J. / Bell, S.G.
History
DepositionDec 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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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)45,5695
Polymers44,6281
Non-polymers9404
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.213, 51.268, 78.417
Angle α, β, γ (deg.)90.00, 92.94, 90.00
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


Mass: 44628.480 Da / Num. of mol.: 1 / Mutation: A248G, G249A, D251Q, 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

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Non-polymers , 5 types, 272 molecules

#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-4MA / 4-METHYLBENZOIC ACID / P-METHYLBENZOIC ACID


Mass: 136.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-E5X / 4-(hydroxymethyl)benzoic acid


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 1.99 Å3/Da / Density % sol: 38.15 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: The crystallization 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: 0.95367 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2023
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: 0.95367 Å / Relative weight: 1
ReflectionResolution: 2.01→44.15 Å / Num. obs: 23259 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.1 / Rrim(I) all: 0.264 / Χ2: 0.49 / Net I/σ(I): 5.4 / Num. measured all: 159873
Reflection shellResolution: 2.01→2.07 Å / % possible obs: 90.6 % / Redundancy: 6.1 % / Rmerge(I) obs: 1.624 / Num. measured all: 9579 / Num. unique obs: 1562 / CC1/2: 0.553 / Rpim(I) all: 0.703 / Rrim(I) all: 1.774 / Χ2: 0.42 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.018→42.894 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 1168 5.04 %
Rwork0.1944 --
obs0.1967 23187 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.018→42.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 65 268 3357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023218
X-RAY DIFFRACTIONf_angle_d0.5694400
X-RAY DIFFRACTIONf_dihedral_angle_d23.1611186
X-RAY DIFFRACTIONf_chiral_restr0.04473
X-RAY DIFFRACTIONf_plane_restr0.004588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0182-2.110.3711440.29912671X-RAY DIFFRACTION97
2.11-2.22120.33891400.26392733X-RAY DIFFRACTION100
2.2212-2.36040.28621430.23552731X-RAY DIFFRACTION100
2.3604-2.54260.28391530.21322749X-RAY DIFFRACTION100
2.5426-2.79850.22641420.2082755X-RAY DIFFRACTION100
2.7985-3.20330.22641490.18312767X-RAY DIFFRACTION100
3.2033-4.03530.18971470.15552774X-RAY DIFFRACTION100
4.0353-42.8940.20191500.15962839X-RAY DIFFRACTION100

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