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- PDB-5uvb: The crystal structure of 4-cyclopropylbenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 5uvb
TitleThe crystal structure of 4-cyclopropylbenzoate-bound CYP199A4
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450 / Substrate
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
4-cyclopropylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsColeman, T. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140103229 Australia
CitationJournal: To Be Published
Title: The crystal structure of 4-cyclopropylbenzoate-bound CYP199A4
Authors: Coleman, T. / Bruning, J.B. / Bell, S.G.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7134
Polymers42,8991
Non-polymers8143
Water9,746541
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.208, 51.309, 79.344
Angle α, β, γ (deg.)90.000, 92.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 / CYP199A4


Mass: 42898.660 Da / Num. of mol.: 1 / Fragment: UNP residues 18-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Production host: Escherichia coli (E. coli) / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-8QM / 4-cyclopropylbenzoic acid


Mass: 162.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O

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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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 23% PEG3350 w/v, 50mM Bis-Tris, pH 5.0, MgAc, 0.2M / PH range: 5.0-5.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.54→43.08 Å / Num. obs: 48030 / % possible obs: 96.8 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.047 / Rrim(I) all: 0.127 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.54-1.566.80.8310970.7180.3340.89645.1
8.41-43.086.40.0380.9980.0160.04298.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.54 Å43.08 Å
Translation1.54 Å43.08 Å

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Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
PHASER2.5.7phasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DO1

4do1


Resolution: 1.54→39.646 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2344 4.88 %Random selection
Rwork0.1424 ---
obs0.1442 48018 96.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 66.12 Å2 / Biso mean: 12.9896 Å2 / Biso min: 4.17 Å2
Refinement stepCycle: final / Resolution: 1.54→39.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 56 541 3618
Biso mean--7.06 23.26 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013167
X-RAY DIFFRACTIONf_angle_d1.384329
X-RAY DIFFRACTIONf_chiral_restr0.049471
X-RAY DIFFRACTIONf_plane_restr0.007574
X-RAY DIFFRACTIONf_dihedral_angle_d14.6751167
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5352-1.56650.235690.19291497156654
1.5665-1.60060.20351520.19452712286498
1.6006-1.63780.25251460.17762699284599
1.6378-1.67880.22011140.17092748286299
1.6788-1.72420.21581330.16872759289299
1.7242-1.77490.21991320.15882746287899
1.7749-1.83220.18111440.15352754289899
1.8322-1.89770.18111490.140227362885100
1.8977-1.97370.18271580.14562727288599
1.9737-2.06350.19171470.137727692916100
2.0635-2.17230.18331620.136227262888100
2.1723-2.30840.16391360.125427732909100
2.3084-2.48660.15351460.129527682914100
2.4866-2.73680.16741380.136228032941100
2.7368-3.13260.16351360.143627892925100
3.1326-3.94620.16121380.128828022940100
3.9462-39.65920.17241440.13628663010100

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