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- PDB-2bwf: Crystal structure of the UBL domain of Dsk2 from S. cerevisiae -

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Basic information

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


Cargo recognition for clathrin-mediated endocytosis / spindle pole body duplication / protein localization to vacuole / K48-linked polyubiquitin modification-dependent protein binding / polyubiquitin modification-dependent protein binding / ERAD pathway / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / nucleus / cytosol
Similarity search - Function
Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site ...Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / : / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Ubiquitin domain-containing protein DSK2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 1.1Apr 15, 2015Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Nov 18, 2020Group: Derived calculations / Other / Structure summary / Category: pdbx_database_status / struct / struct_site
Item: _pdbx_database_status.status_code_sf / _struct.title ..._pdbx_database_status.status_code_sf / _struct.title / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN-LIKE PROTEIN DSK2
B: UBIQUITIN-LIKE PROTEIN DSK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3624
Polymers17,2692
Non-polymers922
Water2,864159
1
A: UBIQUITIN-LIKE PROTEIN DSK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7273
Polymers8,6351
Non-polymers922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: UBIQUITIN-LIKE PROTEIN DSK2


Theoretical massNumber of molelcules
Total (without water)8,6351
Polymers8,6351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.415, 49.587, 58.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UBIQUITIN-LIKE PROTEIN DSK2


Mass: 8634.741 Da / Num. of mol.: 2 / Fragment: UBL DOMAIN, RESIDUES 1-75
Source method: isolated from a genetically manipulated source
Details: UBIQUITIN-LIKE 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: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE STRUCTURE PRESENTED IS OF THE UBL DOMAIN, RESIDUES 1- 75 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 Å3/Da / Density % sol: 38 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.15→37.8 Å / Num. obs: 48617 / % possible obs: 93.8 % / Observed criterion σ(I): 6 / Redundancy: 4.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 3.6
Reflection shellResolution: 1.15→1.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.3 / % possible all: 81.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BT0

1bt0


Resolution: 1.15→34.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 2465 5.1 %RANDOM
Rwork0.184 ---
obs0.185 46148 93.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.83 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.15→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1210 0 6 159 1375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211236
X-RAY DIFFRACTIONr_bond_other_d0.0020.021099
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9371669
X-RAY DIFFRACTIONr_angle_other_deg0.72132590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5445152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021350
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02206
X-RAY DIFFRACTIONr_nbd_refined0.1940.2221
X-RAY DIFFRACTIONr_nbd_other0.2420.21275
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.2695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2461.5770
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90721243
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4313466
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9374.5426
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
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.232 143
Rwork0.23 2805

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