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- PDB-2bwb: Crystal structure of the UBA domain of Dsk2 from S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 2bwb
TitleCrystal structure of the UBA domain of Dsk2 from S. cerevisiae
ComponentsUBIQUITIN-LIKE PROTEIN DSK2
KeywordsSIGNALING PROTEIN / UBIQUITIN / UBA
Function / homology
Function and homology information


Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / polyubiquitin modification-dependent protein binding / ERAD pathway / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / nucleus / cytosol
Similarity search - Function
: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Ubiquitin domain signature. ...: / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Ubiquitin-associated (UBA) domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Helicase, Ruva Protein; domain 3 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ubiquitin domain-containing protein DSK2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLowe, E.D. / Hasan, N. / Trempe, J.-F. / Fonso, L. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N. / Brown, N.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structures of the Dsk2 Ubl and Uba Domains and Their Complex.
Authors: Lowe, E.D. / Hasan, N. / Trempe, J.-F. / Fonso, L. / Noble, M.E.M. / Endicott, J.A. / Johnson, L.N. / Brown, N.R.
History
DepositionJul 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN-LIKE PROTEIN DSK2
B: UBIQUITIN-LIKE PROTEIN DSK2
C: UBIQUITIN-LIKE PROTEIN DSK2
D: UBIQUITIN-LIKE PROTEIN DSK2
E: UBIQUITIN-LIKE PROTEIN DSK2
F: UBIQUITIN-LIKE PROTEIN DSK2
G: UBIQUITIN-LIKE PROTEIN DSK2
H: UBIQUITIN-LIKE PROTEIN DSK2
I: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)46,9329
Polymers46,9329
Non-polymers00
Water2,702150
1
A: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
I: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)5,2151
Polymers5,2151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)116.311, 44.069, 111.525
Angle α, β, γ (deg.)90.00, 114.87, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22I

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A328 - 370
2112B328 - 370
3112C328 - 370
4112D328 - 370
5112E328 - 370
6112F328 - 370
7112G328 - 370
8112H328 - 370
1126A328 - 341
2126I328 - 341
1226A346 - 370
2226I346 - 370

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.82442, 0.47113, 0.31363), (-0.34145, 0.85597, -0.38824), (-0.45137, 0.21299, 0.86655)20.22631, -18.80769, -27.27886
2given(0.3533, 0.85476, 0.38021), (-0.42347, 0.50852, -0.74972), (-0.83418, 0.10387, 0.54162)20.28533, -30.3674, -63.49786
3given(-0.27886, 0.93304, 0.22733), (-0.18159, 0.18122, -0.96653), (-0.94301, -0.31081, 0.11889)3.61382, -27.32594, -98.23232
4given(0.71389, -0.06382, 0.69734), (0.64087, -0.34179, -0.68736), (0.28221, 0.93761, -0.2031)81.21254, -41.14663, -97.40068
5given(0.32668, 0.40288, 0.85496), (0.93935, -0.03846, -0.3408), (-0.10442, 0.91444, -0.39101)78.56183, -6.55663, -103.46541
6given(-0.26529, 0.61272, 0.74444), (0.91818, 0.39616, 0.00115), (-0.29421, 0.68384, -0.66769)56.53645, 21.73804, -111.19116
7given(-0.79746, 0.42199, 0.43127), (0.53146, 0.82966, 0.17092), (-0.28568, 0.36551, -0.88589)23.09112, 32.64115, -111.89786
8given(-0.7199, 0.61842, -0.31512), (0.24703, -0.19599, -0.94898), (-0.64863, -0.76102, -0.01168)-29.08712, 32.64115, -111.89786

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Components

#1: Protein/peptide
UBIQUITIN-LIKE PROTEIN DSK2


Mass: 5214.702 Da / Num. of mol.: 9 / Fragment: UBA DOMAIN, RESIDUES 326-371
Source method: isolated from a genetically manipulated source
Details: UBIQUITIN BINDING DOMAIN OF DSK2 PROTEIN
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGEX-KG / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3)PLYSS / References: UniProt: P48510
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE STRUCTURE PRESENTED IS OF THE UBA DOMAIN, RESIDUES 326- 371 OF THE INTACT PROTEIN

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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: 2.4 Å3/Da / Density % sol: 48.3 %
Crystal growpH: 7.5 / Details: 1.6 M TRISODIUM CITRATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: May 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→29.5 Å / Num. obs: 23134 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.4
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→101.02 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.904 / SU B: 22.554 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.353 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1127 4.9 %RANDOM
Rwork0.243 ---
obs0.246 22007 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→101.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 0 150 3337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213230
X-RAY DIFFRACTIONr_bond_other_d0.0020.022844
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9524326
X-RAY DIFFRACTIONr_angle_other_deg0.82836553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9975388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92823.738214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54415539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.231545
X-RAY DIFFRACTIONr_chiral_restr0.0620.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023758
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02743
X-RAY DIFFRACTIONr_nbd_refined0.20.2696
X-RAY DIFFRACTIONr_nbd_other0.1730.22734
X-RAY DIFFRACTIONr_nbtor_refined0.170.21514
X-RAY DIFFRACTIONr_nbtor_other0.0870.22028
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.259
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.2176
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3571.52478
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.42223055
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.74131408
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1514.51271
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A253tight positional0.050.05
12B253tight positional0.030.05
13C253tight positional0.040.05
14D253tight positional0.040.05
15E253tight positional0.040.05
16F253tight positional0.030.05
17G253tight positional0.030.05
18H253tight positional0.030.05
11A402medium positional0.820.5
12B402medium positional0.710.5
13C402medium positional0.80.5
14D402medium positional0.730.5
15E402medium positional0.620.5
16F402medium positional0.70.5
17G402medium positional0.690.5
18H402medium positional0.740.5
21A579loose positional0.745
11A253tight thermal0.060.5
12B253tight thermal0.060.5
13C253tight thermal0.070.5
14D253tight thermal0.050.5
15E253tight thermal0.10.5
16F253tight thermal0.050.5
17G253tight thermal0.050.5
18H253tight thermal0.060.5
11A402medium thermal0.352
12B402medium thermal0.272
13C402medium thermal0.312
14D402medium thermal0.252
15E402medium thermal0.52
16F402medium thermal0.342
17G402medium thermal0.252
18H402medium thermal0.282
21A579loose thermal1.4810
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 83
Rwork0.306 1576

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