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- PDB-3l3f: Crystal structure of a PFU-PUL domain pair of Saccharomyces cerev... -

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Basic information

Entry
Database: PDB / ID: 3l3f
TitleCrystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3
ComponentsProtein DOA1
KeywordsPROTEIN BINDING / Armadillo-like repeat structure / Nucleus / Ubl conjugation pathway
Function / homology
Function and homology information


ribophagy / Neddylation / cytoplasmic side of mitochondrial outer membrane / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin recycling / ubiquitin-dependent protein binding / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / double-strand break repair via nonhomologous end joining ...ribophagy / Neddylation / cytoplasmic side of mitochondrial outer membrane / mitochondria-associated ubiquitin-dependent protein catabolic process / ubiquitin recycling / ubiquitin-dependent protein binding / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / double-strand break repair via nonhomologous end joining / endosome membrane / protein-containing complex binding / nucleus / cytoplasm
Similarity search - Function
PFU (PLAA family ubiquitin binding), C-terminal domain / PUL domain profile. / PFU domain profile. / PFU (PLAA family ubiquitin binding) / PUL domain / PFU domain superfamily / PLAA family ubiquitin binding domain / PUL domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...PFU (PLAA family ubiquitin binding), C-terminal domain / PUL domain profile. / PFU domain profile. / PFU (PLAA family ubiquitin binding) / PUL domain / PFU domain superfamily / PLAA family ubiquitin binding domain / PUL domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / G-protein beta WD-40 repeat / Ubiquitin-like (UB roll) / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / : / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Armadillo-type fold / Alpha Horseshoe / WD40/YVTN repeat-like-containing domain superfamily / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKomori, H. / Nishimasu, R. / Kuno, T. / Higuchi, Y.
CitationJournal: KOBE J.MED.SCI. / Year: 2010
Title: Crystal Structure of a PFU-PUL Domain Pair of Saccharomyces Cerevisiae Doa1/Ufd3
Authors: Nishimasu, R. / Komori, H. / Higuchi, Y. / Nishimasu, H. / Hiroaki, H.
History
DepositionDec 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Protein DOA1


Theoretical massNumber of molelcules
Total (without water)40,8141
Polymers40,8141
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)103.115, 103.115, 72.117
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Protein DOA1 / Doa1/Ufd3


Mass: 40814.117 Da / Num. of mol.: 1 / Fragment: PFU-PUL domain, residues 354-715
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P36037
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris-HCl (pH 7.5), 28% PEG 3350, 0.1M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9789, 0.9792, 0.9640
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97921
30.9641
ReflectionResolution: 1.9→33.75 Å / Num. obs: 34591 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.256 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
SHARPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→33.426 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.784 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21877 1726 5 %RANDOM
Rwork0.19472 ---
obs0.19594 32712 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å20 Å2
2---0.46 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 214 2757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222594
X-RAY DIFFRACTIONr_bond_other_d0.0010.022332
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9663525
X-RAY DIFFRACTIONr_angle_other_deg0.77835451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54525.68125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7315455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.646159
X-RAY DIFFRACTIONr_chiral_restr0.0640.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
X-RAY DIFFRACTIONr_nbd_refined0.2090.2560
X-RAY DIFFRACTIONr_nbd_other0.1620.22304
X-RAY DIFFRACTIONr_nbtor_refined0.180.21305
X-RAY DIFFRACTIONr_nbtor_other0.080.21452
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0781.51991
X-RAY DIFFRACTIONr_mcbond_other0.1511.5633
X-RAY DIFFRACTIONr_mcangle_it1.28522572
X-RAY DIFFRACTIONr_scbond_it1.98631166
X-RAY DIFFRACTIONr_scangle_it2.9024.5953
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 121 -
Rwork0.215 2422 -
obs--100 %

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