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- PDB-7udf: The crystal structure of F298V CYP199A4 bound to 4-n-propylbenzoi... -

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Basic information

Entry
Database: PDB / ID: 7udf
TitleThe crystal structure of F298V CYP199A4 bound to 4-n-propylbenzoic acid
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Mutant cytochrome P450 enzyme
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-propylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsPodgorski, M.N. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Chem Asian J / Year: 2022
Title: Exploring the Factors which Result in Cytochrome P450 Catalyzed Desaturation Versus Hydroxylation.
Authors: Coleman, T. / Doherty, D.Z. / Zhang, T. / Podgorski, M.N. / Qiao, R. / Lee, J.H.Z. / Bruning, J.B. / De Voss, J.J. / Zhou, W. / Bell, S.G.
History
DepositionMar 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)45,3564
Polymers44,5391
Non-polymers8163
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.491, 51.395, 78.779
Angle α, β, γ (deg.)90.000, 92.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 44539.387 Da / Num. of mol.: 1 / Mutation: F298V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris HaA2 (phototrophic)
Strain: HaA2 / 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-8ZU / 4-propylbenzoic acid


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2 / 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.: 476 / 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: 2.02 Å3/Da / Density % sol: 39.11 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: For crystallisation, F298V CYP199A4 was concentrated to approx. 30-40 mg mL-1 in 50 mM Tris, pH 7.4. The crystallisation buffer was 100 mM Bis-Tris buffer (adjusted to pH 5.0-5.75 with ...Details: For crystallisation, F298V CYP199A4 was concentrated to approx. 30-40 mg mL-1 in 50 mM Tris, pH 7.4. 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: 5.00-5.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 29, 2021
RadiationMonochromator: Double-crystal Si(111) water-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.54→44.44 Å / Num. obs: 52262 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 17.09 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 11.9 / Num. measured all: 364962 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.54-1.576.91.281697724720.8010.521.3841.296.4
8.44-44.446.80.013235834610.0050.0146299.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.84 Å44.44 Å
Translation5.84 Å44.44 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PHENIX1.11.1-2575refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UVB

5uvb


Resolution: 1.54→39.348 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 2005 3.84 %
Rwork0.1806 50191 -
obs0.1822 52196 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.13 Å2 / Biso mean: 26.0878 Å2 / Biso min: 14.28 Å2
Refinement stepCycle: final / Resolution: 1.54→39.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 67 477 3561
Biso mean--21.16 35.97 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123198
X-RAY DIFFRACTIONf_angle_d1.174375
X-RAY DIFFRACTIONf_chiral_restr0.065475
X-RAY DIFFRACTIONf_plane_restr0.008583
X-RAY DIFFRACTIONf_dihedral_angle_d24.3811180
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5405-1.5790.36021410.3521350397
1.579-1.62170.35981490.3207357499
1.6217-1.66940.33611320.3022356199
1.6694-1.72330.3621460.277357299
1.7233-1.78490.30731400.2573359199
1.7849-1.85640.3061400.2336354599
1.8564-1.94080.28651450.2082357399
1.9408-2.04320.2751400.2005351098
2.0432-2.17120.24751490.18543585100
2.1712-2.33880.20641410.16783676100
2.3388-2.57410.20771410.17043575100
2.5741-2.94650.20971470.17273643100
2.9465-3.71180.1861430.1484356998
3.7118-39.3480.15741510.13173714100

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