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- PDB-6prs: The crystal structure of 3-ethoxybenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6prs
TitleThe crystal structure of 3-ethoxybenzoate-bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / 3-ethoxybenzoic acid
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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 3-ethoxybenzoic acid / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.373 Å
AuthorsPodgorski, M.N. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 and ANSTO Australian Synchrotron Collaborative Access Program (CAP) grant MXCAP13667/14238 Australia
CitationJournal: J.Inorg.Biochem. / Year: 2019
Title: Investigation of the requirements for efficient and selective cytochrome P450 monooxygenase catalysis across different reactions.
Authors: Podgorski, M.N. / Coleman, T. / Chao, R.R. / De Voss, J.J. / Bruning, J.B. / Bell, S.G.
History
DepositionJul 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4064
Polymers44,5871
Non-polymers8183
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-37 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.592, 51.416, 79.365
Angle α, β, γ (deg.)90.000, 92.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 44587.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain 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-OW7 / 3-ethoxybenzoic acid


Mass: 166.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O3 / 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.: 210 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M magnesium acetate, 100 mM Bis-Tris adjusted with acetic acid to pH 5.0-5.75, 20-32% w/v PEG3350
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: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2018
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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.37→44.56 Å / Num. obs: 14637 / % possible obs: 98.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 19.58 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.083 / Rrim(I) all: 0.21 / Net I/σ(I): 5.8 / Num. measured all: 91049 / Scaling rejects: 48
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
2.37-2.455.20.75674813100.7030.3570.8341.584.1
8.85-44.566.10.08818663060.9610.0390.09716.599.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.83 Å44.56 Å
Translation5.83 Å44.56 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.2data scaling
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UVB

5uvb


Resolution: 2.373→44.559 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.22
RfactorNum. reflection% reflection
Rfree0.2219 1454 9.97 %
Rwork0.1825 --
obs0.1863 14580 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 56.77 Å2 / Biso mean: 28.0124 Å2 / Biso min: 19.94 Å2
Refinement stepCycle: final / Resolution: 2.373→44.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 56 210 3287
Biso mean--23.78 28.42 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023167
X-RAY DIFFRACTIONf_angle_d0.6084326
X-RAY DIFFRACTIONf_chiral_restr0.04470
X-RAY DIFFRACTIONf_plane_restr0.004574
X-RAY DIFFRACTIONf_dihedral_angle_d8.492605
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.373-2.45730.26831240.2431118089
2.4573-2.55570.27471480.2321314100
2.5557-2.6720.26141440.2321291100
2.672-2.81290.28931500.22731331100
2.8129-2.98910.25061400.20981318100
2.9891-3.21980.24421560.19641328100
3.2198-3.54370.21411440.18161310100
3.5437-4.05620.19221470.15581348100
4.0562-5.10920.17531490.14231331100
5.1092-44.5590.20291520.15631375100

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