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- PDB-5kdb: The crystal structure of 4-isopropylbenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 5kdb
TitleThe crystal structure of 4-isopropylbenzoate-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-propan-2-ylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.644 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-isopropylbenzoate-bound CYP199A4
Authors: Coleman, T. / Bruning, J.B. / Bell, S.G.
History
DepositionJun 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 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)43,7154
Polymers42,8991
Non-polymers8163
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.313, 51.453, 79.283
Angle α, β, γ (deg.)90.000, 91.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450 /


Mass: 42898.660 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 (E. coli) / References: UniProt: Q2IU02
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-4IA / 4-propan-2-ylbenzoic acid


Mass: 164.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.11 Å3/Da / Density % sol: 41.59 % / Description: Rectangular plates, good thickness.
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M Magnesium acetate PEG 3350 - 23% w/v 0.1M Bis-Tris, pH 5.5
PH range: 5.25 - 6 / Temp details: 16 degrees C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.64→44.29 Å / Num. obs: 43487 / % possible obs: 99.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 13.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.122 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.64-1.676.80.81192.3
9-44.296.70.032199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.5.21data scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 4DO1

4do1


Resolution: 1.644→43.154 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.65
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 1998 4.6 %Randomly selected.
Rwork0.1466 ---
obs0.1484 43470 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.57 Å2 / Biso mean: 18.1195 Å2 / Biso min: 5.5 Å2
Refinement stepCycle: final / Resolution: 1.644→43.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 97 483 3601
Biso mean--10.55 31.46 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013167
X-RAY DIFFRACTIONf_angle_d1.3514324
X-RAY DIFFRACTIONf_chiral_restr0.048469
X-RAY DIFFRACTIONf_plane_restr0.008572
X-RAY DIFFRACTIONf_dihedral_angle_d12.8011165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6435-1.68460.24971270.21562832295997
1.6846-1.73020.26631520.200729493101100
1.7302-1.78110.22831340.176429673101100
1.7811-1.83860.21161470.176229593106100
1.8386-1.90430.19011430.164529253068100
1.9043-1.98060.2021470.162929723119100
1.9806-2.07070.22991370.152329553092100
2.0707-2.17990.17761460.14529523098100
2.1799-2.31640.16641410.134329833124100
2.3164-2.49530.1961420.132529713113100
2.4953-2.74630.16111380.141629593097100
2.7463-3.14360.19091440.147529873131100
3.1436-3.96020.16091500.127429933143100
3.9602-43.16860.17321500.134730683218100

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