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- PDB-3uc9: Crystal Structure of Yeast Irc6p - A Novel Type of Conserved Clat... -

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Basic information

Entry
Database: PDB / ID: 3uc9
TitleCrystal Structure of Yeast Irc6p - A Novel Type of Conserved Clathrin Accessory Protein
ComponentsIncreased recombination centers protein 6
KeywordsRECOMBINATION / Rossmann-fold / Clathrin accessory factor
Function / homologyRossmann fold - #11960 / Increased recombination centres protein 6 / vesicle-mediated transport / protein-macromolecule adaptor activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Increased recombination centers protein 6
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsGorynia, S. / Payne, G.S. / Cascio, D. / Sawaya, M.R.
CitationJournal: Mol Biol Cell / Year: 2012
Title: Yeast Irc6p is a novel type of conserved clathrin coat accessory factor related to small G proteins.
Authors: Gorynia, S. / Lorenz, T.C. / Costaguta, G. / Daboussi, L. / Cascio, D. / Payne, G.S.
History
DepositionOct 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Increased recombination centers protein 6


Theoretical massNumber of molelcules
Total (without water)27,4191
Polymers27,4191
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.638, 61.638, 95.144
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Increased recombination centers protein 6


Mass: 27419.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: IRC6, YFR043C / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43615
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.9 Å3/Da / Density % sol: 35.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 MES, 30 % w/v PEG monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 18511 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 14.74 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.006 / Net I/σ(I): 13.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.8-1.867.80.5413.9618171.0196.5
1.86-1.947.80.3525.7818281.00796.9
1.94-2.037.80.244818341.00896.9
2.03-2.137.70.1899.6418571.00697.4
2.13-2.277.50.13812.3918611.00697.5
2.27-2.447.30.11413.8518301.00497.8
2.44-2.696.90.08815.8218781.00398.2
2.69-3.086.30.05819.4918601.00698
3.08-3.885.10.03229.041871198.2
3.88-804.80.02345.2718751.00296.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→27.27 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.374 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 963 5.2 %RANDOM
Rwork0.1966 ---
obs0.1977 18510 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.24 Å2 / Biso mean: 25.72 Å2 / Biso min: 4.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.119 Å0.134 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 0 40 1538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221534
X-RAY DIFFRACTIONr_bond_other_d0.0010.02991
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.922089
X-RAY DIFFRACTIONr_angle_other_deg0.81732429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7135178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66325.69886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41115262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.329155
X-RAY DIFFRACTIONr_chiral_restr0.0690.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02298
X-RAY DIFFRACTIONr_mcbond_it1.1221.5900
X-RAY DIFFRACTIONr_mcbond_other0.3411.5357
X-RAY DIFFRACTIONr_mcangle_it2.06521476
X-RAY DIFFRACTIONr_scbond_it3.2533634
X-RAY DIFFRACTIONr_scangle_it5.1774.5613
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 64 -
Rwork0.223 1260 -
all-1324 -
obs--96.01 %
Refinement TLS params.Method: refined / Origin x: 32.8344 Å / Origin y: 17.5676 Å / Origin z: -7.1722 Å
111213212223313233
T0.0197 Å2-0.013 Å20.0015 Å2-0.0245 Å2-0.0126 Å2--0.0529 Å2
L0.9316 °20.0123 °2-0.7714 °2-1.3807 °20.0869 °2--1.7464 °2
S-0.0388 Å °0.0201 Å °-0.0437 Å °0.1026 Å °0.0376 Å °-0.0241 Å °0.0539 Å °-0.0383 Å °0.0012 Å °

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