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- PDB-6c3h: The crystal structure of 4-n-heptylbenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6c3h
TitleThe crystal structure of 4-n-heptylbenzoate-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-heptylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.705 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-n-heptylbenzoate-bound CYP199A4
Authors: Coleman, T. / Bruning, J.B. / Bell, S.G.
History
DepositionJan 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: 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)43,7714
Polymers42,8991
Non-polymers8723
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.539, 51.392, 78.538
Angle α, β, γ (deg.)90.000, 92.650, 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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-EJV / 4-heptylbenzoic acid


Mass: 220.307 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20O2
#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.: 485 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: McAc, 0.2M Bis-Tris, 0.1M, pH 5.5 PEG-3350, 26 % w/v
PH range: 5.25-6.0 / Temp details: 16 C

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.705→44.491 Å / Num. obs: 38417 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.32 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.082 / Net I/σ(I): 19.7
Reflection shellResolution: 1.705→1.7506 Å / Rmerge(I) obs: 0.777 / Rpim(I) all: 0.482

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.7 Å44.49 Å
Translation1.7 Å44.49 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.5.7phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KDB

5kdb


Resolution: 1.705→44.491 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.28
RfactorNum. reflection% reflectionSelection details
Rfree0.2111 1857 4.84 %Random selection
Rwork0.1738 ---
obs0.1756 38387 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.33 Å2 / Biso mean: 22.5525 Å2 / Biso min: 11.01 Å2
Refinement stepCycle: final / Resolution: 1.705→44.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 60 486 3567
Biso mean--17.01 31.79 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123185
X-RAY DIFFRACTIONf_angle_d1.3364352
X-RAY DIFFRACTIONf_chiral_restr0.073472
X-RAY DIFFRACTIONf_plane_restr0.008577
X-RAY DIFFRACTIONf_dihedral_angle_d23.9171182
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.705-1.75060.33251200.2682246688
1.7506-1.80210.26531650.24652816100
1.8021-1.86030.30711580.23692799100
1.8603-1.92680.27191620.21452799100
1.9268-2.00390.26961530.20552840100
2.0039-2.09510.23641160.19322840100
2.0951-2.20560.26041410.18742826100
2.2056-2.34380.2361680.17782846100
2.3438-2.52470.22031430.17712811100
2.5247-2.77880.21791290.17822873100
2.7788-3.18080.20771300.17132873100
3.1808-4.0070.1611410.1435283098
4.007-44.4910.14421310.1413291199

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