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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 / Oxidoreductase / Substrate
Function / homologyCytochrome P450 / Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 superfamily / Cytochrome P450 / Cytochrome P450 cysteine heme-iron ligand signature. / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / Cytochrome P450
Function and homology information
Specimen sourceRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 1.705 Å resolution
AuthorsColeman, T. / Bruning, J.B. / Bell, S.G.
Funding supportAustralia , 1 items
OrganizationGrant numberCountry
Australian Research CouncilDP140103229Australia
CitationJournal: To Be Published
Title: The crystal structure of 4-n-heptylbenzoate-bound CYP199A4
Authors: Coleman, T. / Bruning, J.B. / Bell, S.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 9, 2018 / Release: Jan 16, 2019

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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
Polyers42,8991
Non-polymers8723
Water8,737485
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
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-MP 1 21 1

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Components

#1: Protein/peptide Cytochrome P450 /


Mass: 42898.660 Da / Num. of mol.: 1
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 / Formula: C34H32FeN4O4 / Heme
#3: Chemical ChemComp-EJV / 4-heptylbenzoic acid


Mass: 220.307 Da / Num. of mol.: 1 / Formula: C14H20O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Formula: Cl / Chloride
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / Formula: H2O / Water

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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 / Density percent sol: 41.23 %
Crystal growTemp: 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 kelvins / Ambient temp details: 100 K
SourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Collection date: Apr 19, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 18.32 Å2 / D resolution high: 1.705 Å / D resolution low: 44.491 Å / Number obs: 38417 / Rmerge I obs: 0.142 / Rpim I all: 0.082 / NetI over sigmaI: 19.7 / Redundancy: 4.1 % / Percent possible obs: 99.4
Reflection shellRmerge I obs: 0.777 / Highest resolution: 1.705 Å / Lowest resolution: 1.7506 Å / Rpim I all: 0.482

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Phasing

PhasingMethod: molecular replacement
Phasing MRD res high rotation: 1.7 / D res high translation: 1.7 / D res low rotation: 44.49 / D res low translation: 44.49 / Model details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationContact authorContact author emailLocationTypeDateLanguage
HKL-2000data reductionZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/package
SCALEPACKdata scalingZbyszek Otwinowskihkl[at]hkl-xray.comhttp://www.hkl-xray.com/program
PHASER2.5.7phasingRandy J. Readcimr-phaser[at]lists.cam.ac.ukhttp://www-structmed.cimr.cam.ac.uk/phaser/programTue May 26 15:08:19 2015
PHENIXrefinementPaul D. AdamsPDAdams[at]lbl.govhttp://www.phenix-online.org/packageC++
PDB_EXTRACT3.24data extractionPDBdeposit[at]deposit.rcsb.orghttp://sw-tools.pdb.org/apps/PDB_EXTRACT/packageSep. 1, 2017C++
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KDB
Overall SU ML: 0.2 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 23.28
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 81.33 Å2 / B iso mean: 22.5525 Å2 / B iso min: 11.01 Å2
Least-squares processR factor R free: 0.2111 / R factor R work: 0.1738 / R factor obs: 0.1756 / Highest resolution: 1.705 Å / Lowest resolution: 44.491 Å / Number reflection R free: 1857 / Number reflection obs: 38387 / Percent reflection R free: 4.84 / Percent reflection obs: 98.73
Refine hist #finalHighest resolution: 1.705 Å / Lowest resolution: 44.491 Å / B iso mean ligand: 17.01 / B iso mean solvent: 31.79 / Number residues total: 393
Number of atoms included #finalProtein: 3021 / Nucleic acid: 0 / Ligand: 60 / Solvent: 486 / Total: 3567
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
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
1.70500.33250.26821.7506120246688.0000
1.75060.26530.24651.80211652816100.0000
1.80210.30710.23691.86031582799100.0000
1.86030.27190.21451.92681622799100.0000
1.92680.26960.20552.00391532840100.0000
2.00390.23640.19322.09511162840100.0000
2.09510.26040.18742.20561412826100.0000
2.20560.23600.17782.34381682846100.0000
2.34380.22030.17712.52471432811100.0000
2.52470.21790.17822.77881292873100.0000
2.77880.20770.17133.18081302873100.0000
3.18080.16100.14354.0070141283098.0000
4.00700.14420.141344.4910131291199.0000

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