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- PDB-8vf3: The crystal structure of GALQE CYP199A4 bound to 4-methoxybenzoic acid -

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Basic information

Entry
Database: PDB / ID: 8vf3
TitleThe crystal structure of GALQE CYP199A4 bound to 4-methoxybenzoic acid
ComponentsCytochrome P450 enzyme (CYP199A4)
KeywordsOXIDOREDUCTASE / Cytochrome P450 peroxygenase
Function / homologyACETATE ION / 4-METHOXYBENZOIC ACID / PROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.469 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 enzyme (CYP199A4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5166
Polymers44,6281
Non-polymers8875
Water12,881715
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.085, 51.530, 78.520
Angle α, β, γ (deg.)90.00, 93.53, 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 enzyme (CYP199A4)


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)
Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 720 molecules

#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: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
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: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2022
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: 1.469→45 Å / Num. obs: 60758 / % possible obs: 99.1 % / Redundancy: 5.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.049 / Rrim(I) all: 0.122 / Χ2: 0.6 / Net I/σ(I): 7.5
Reflection shellResolution: 1.47→1.49 Å / % possible obs: 95.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.545 / Num. measured all: 15554 / Num. unique obs: 2902 / CC1/2: 0.84 / Rpim(I) all: 0.248 / Rrim(I) all: 0.601 / Χ2: 0.6 / Net I/σ(I) obs: 2.7

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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: 1.469→45 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1726 1992 3.28 %
Rwork0.1529 --
obs0.1536 60704 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.469→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 60 715 3799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063253
X-RAY DIFFRACTIONf_angle_d0.8394452
X-RAY DIFFRACTIONf_dihedral_angle_d25.2581201
X-RAY DIFFRACTIONf_chiral_restr0.072479
X-RAY DIFFRACTIONf_plane_restr0.006596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.469-1.50570.20791370.18274112X-RAY DIFFRACTION97
1.5057-1.54640.20891450.16644174X-RAY DIFFRACTION99
1.5464-1.59190.20791400.16184192X-RAY DIFFRACTION99
1.5919-1.64330.19171330.15494158X-RAY DIFFRACTION99
1.6433-1.7020.18131390.15494187X-RAY DIFFRACTION99
1.702-1.77020.19251540.15054168X-RAY DIFFRACTION99
1.7702-1.85070.17461480.14564216X-RAY DIFFRACTION99
1.8507-1.94830.1581410.14264178X-RAY DIFFRACTION99
1.9483-2.07040.15451370.1434215X-RAY DIFFRACTION99
2.0704-2.23020.16711490.14084191X-RAY DIFFRACTION99
2.2302-2.45460.19291410.15134171X-RAY DIFFRACTION98
2.4546-2.80980.17851430.16034194X-RAY DIFFRACTION99
2.8098-3.53980.14851460.15954217X-RAY DIFFRACTION99
3.5398-450.16721390.14974339X-RAY DIFFRACTION99

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