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- PDB-4goc: Crystal structure of the Get5 ubiquitin-like domain -

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Basic information

Entry
Database: PDB / ID: 4goc
TitleCrystal structure of the Get5 ubiquitin-like domain
ComponentsGolgi to ER traffic protein 5
KeywordsPROTEIN BINDING / ubiquitin-like domain / protein-protein interaction / Sgt2
Function / homology
Function and homology information


cell morphogenesis involved in conjugation with cellular fusion / TRC complex / protein insertion into ER membrane / post-translational protein targeting to endoplasmic reticulum membrane / cytoplasmic stress granule / nucleus / cytosol / cytoplasm
Similarity search - Function
Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Get5 C-terminal domain / : / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. ...Mdy2, Get4 binding domain / Get5, C-terminal domain / Binding domain to Get4 on Get5, Golgi to ER traffic protein / Get5 C-terminal domain / : / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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
Ubiquitin-like protein MDY2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChartron, J.W. / VanderVelde, D.G. / Clemons Jr., W.M.
CitationJournal: Cell Rep / Year: 2012
Title: Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved Dynamic Interface.
Authors: Chartron, J.W. / Vandervelde, D.G. / Clemons, W.M.
History
DepositionAug 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Jan 16, 2013Group: Database references
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
A: Golgi to ER traffic protein 5
B: Golgi to ER traffic protein 5
C: Golgi to ER traffic protein 5


Theoretical massNumber of molelcules
Total (without water)25,6323
Polymers25,6323
Non-polymers00
Water1,874104
1
A: Golgi to ER traffic protein 5


Theoretical massNumber of molelcules
Total (without water)8,5441
Polymers8,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Golgi to ER traffic protein 5


Theoretical massNumber of molelcules
Total (without water)8,5441
Polymers8,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Golgi to ER traffic protein 5


Theoretical massNumber of molelcules
Total (without water)8,5441
Polymers8,5441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.360, 63.620, 71.580
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 Golgi to ER traffic protein 5 / Ubiquitin-like protein MDY2 / Mating-deficient protein 2 / Translation machinery-associated protein 24


Mass: 8544.010 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GET5, MDY2, TMA24, YOL111C / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): NiCo(DE3) / References: UniProt: Q12285
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2012
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→29.07 Å / Num. obs: 9092 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 6.6
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.8 / Num. unique all: 666 / % possible all: 98.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1066)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.069 Å / SU ML: 0.39 / σ(F): 2.03 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 907 9.98 %RANDOM
Rwork0.1737 ---
obs0.1809 9084 98.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 0 104 1907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071833
X-RAY DIFFRACTIONf_angle_d1.1032475
X-RAY DIFFRACTIONf_dihedral_angle_d15.186693
X-RAY DIFFRACTIONf_chiral_restr0.07312
X-RAY DIFFRACTIONf_plane_restr0.005300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.55040.35051490.24811340X-RAY DIFFRACTION99
2.5504-2.74720.29981490.23741340X-RAY DIFFRACTION98
2.7472-3.02340.30531480.21521337X-RAY DIFFRACTION99
3.0234-3.46020.31061510.17041357X-RAY DIFFRACTION99
3.4602-4.35720.17971510.12861372X-RAY DIFFRACTION98
4.3572-29.0710.19291590.15711431X-RAY DIFFRACTION97

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