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- PDB-1otk: Structural Genomics, Protein paaC -

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Basic information

Entry
Database: PDB / ID: 1otk
TitleStructural Genomics, Protein paaC
ComponentsPhenylacetic acid degradation protein paaC
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phenylacetyl-CoA 1,2-epoxidase complex / phenylacetate catabolic process / cytosol
Similarity search - Function
1,2-phenylacetyl-CoA epoxidase, subunit C / 1,2-phenylacetyl-CoA epoxidase, subunit A/C / Phenylacetic acid catabolic protein / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-phenylacetyl-CoA epoxidase, subunit C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Skarina, T. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 2 A crystal structure of protein paaC from E. Coli
Authors: Zhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Skarina, T.
History
DepositionMar 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenylacetic acid degradation protein paaC
B: Phenylacetic acid degradation protein paaC


Theoretical massNumber of molelcules
Total (without water)55,9392
Polymers55,9392
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-12 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.216, 95.707, 127.088
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein exists as dimer which consists of molA and molB.

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Components

#1: Protein Phenylacetic acid degradation protein paaC / PROTEIN PAAC


Mass: 27969.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: PAAC OR B1390 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: P76079
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11% iso-Prop., 0.1 M Nacacod., 0.2M NaCitr., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 17, 2003 / Details: Si 111 Channel
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 49792 / Num. obs: 49742 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.76 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 33.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 5.84 / Num. unique all: 4898 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS0.9refinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→46.82 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: The number of reflections for refinement includes Freidel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4511 4.9 %RANDOM
Rwork0.194 ---
obs0.194 91936 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.7366 Å2 / ksol: 0.34617 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å20 Å20 Å2
2--3.8 Å20 Å2
3----0.57 Å2
Refine analyzeLuzzati coordinate error free: 0.25 Å / Luzzati sigma a free: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 0 342 4195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.245 711 4.9 %
Rwork0.245 13916 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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