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- PDB-6c2d: The crystal structure of 4-cyclohexylbenzoate-bound CYP199A4 -

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Basic information

Entry
Database: PDB / ID: 6c2d
TitleThe crystal structure of 4-cyclohexylbenzoate-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-cyclohexylbenzoic acid / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodopseudomonas palustris HaA2 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 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-cyclohexylbenzoate-bound CYP199A4
Authors: Coleman, T. / Bruning, J.B. / Bell, S.G.
History
DepositionJan 8, 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)43,7554
Polymers42,8991
Non-polymers8563
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.145, 51.438, 79.673
Angle α, β, γ (deg.)90.000, 91.970, 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 HaA2 (phototrophic)
Strain: HaA2 / Gene: RPB_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2IU02
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-EH1 / 4-cyclohexylbenzoic acid


Mass: 204.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 41.63 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: PEG 3350, 23 % w/v Bis-Tris, 0.1M, pH 5.25 MgAc, 0.2M
PH range: 5.25-6.0

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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: Nov 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.79→44.12 Å / Num. obs: 33615 / % possible obs: 98.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.43 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.057 / Rrim(I) all: 0.156 / Net I/σ(I): 11 / Num. measured all: 249404
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.833 / Num. measured all: 10241 / Num. unique obs: 1483 / CC1/2: 0.766 / Rpim(I) all: 0.333 / Rrim(I) all: 0.899 / Net I/σ(I) obs: 2 / % possible all: 76.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.79 Å44.12 Å
Translation6.6 Å44.12 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
Aimless0.5.25data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KDB

5kdb


Resolution: 1.79→39.813 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 1655 4.93 %Random selection
Rwork0.1453 31944 --
obs0.1473 33599 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.27 Å2 / Biso mean: 15.4964 Å2 / Biso min: 4.99 Å2
Refinement stepCycle: final / Resolution: 1.79→39.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3021 0 59 565 3645
Biso mean--9.16 26.21 -
Num. residues----393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113177
X-RAY DIFFRACTIONf_angle_d1.254343
X-RAY DIFFRACTIONf_chiral_restr0.055472
X-RAY DIFFRACTIONf_plane_restr0.007576
X-RAY DIFFRACTIONf_dihedral_angle_d23.4541176
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.79-1.83940.29611190.22152261238084
1.8394-1.89870.22321430.192226632806100
1.8987-1.96660.24461380.169226542792100
1.9666-2.04530.22671370.160127012838100
2.0453-2.13840.1941290.150426802809100
2.1384-2.25110.19351430.144427042847100
2.2511-2.39220.18791510.137826582809100
2.3922-2.57680.18341290.142227262855100
2.5768-2.83610.19851380.149426952833100
2.8361-3.24630.20081410.144726932834100
3.2463-4.08930.14161290.121227362865100
4.0893-39.82270.14331580.131227732931100

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