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- PDB-2vyi: Crystal Structure of the TPR domain of Human SGT -

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Basic information

Entry
Database: PDB / ID: 2vyi
TitleCrystal Structure of the TPR domain of Human SGT
ComponentsSGTA PROTEIN
KeywordsCHAPERONE / SGT / TPR REPEAT / PHOSPHOPROTEIN / TETRATRICOPEPTIDE REPEAT PROTEIN / HOST-VIRUS INTERACTION
Function / homology
Function and homology information


positive regulation of chaperone-mediated protein folding / : / : / TRC complex / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / extrinsic component of synaptic vesicle membrane / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of ubiquitin-dependent protein catabolic process / BAT3 complex binding ...positive regulation of chaperone-mediated protein folding / : / : / TRC complex / positive regulation of ERAD pathway / tail-anchored membrane protein insertion into ER membrane / extrinsic component of synaptic vesicle membrane / post-translational protein targeting to endoplasmic reticulum membrane / positive regulation of ubiquitin-dependent protein catabolic process / BAT3 complex binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / : / viral process / negative regulation of ubiquitin-dependent protein catabolic process / : / molecular adaptor activity / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / : / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. ...SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / : / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Small glutamine-rich tetratricopeptide repeat-containing protein alpha / Small glutamine-rich tetratricopeptide repeat-containing protein alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDutta, S. / Tan, Y.J.
CitationJournal: Biochemistry / Year: 2008
Title: Structural and Functional Characterization of Human Sgt and its Interaction with Vpu of the Human Immunodeficiency Virus Type 1.
Authors: Dutta, S. / Tan, Y.J.
History
DepositionJul 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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: SGTA PROTEIN
B: SGTA PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,8602
Polymers28,8602
Non-polymers00
Water3,243180
1
A: SGTA PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,4301
Polymers14,4301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SGTA PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,4301
Polymers14,4301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.823, 81.939, 55.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein SGTA PROTEIN / / SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEAT 1 / SMALL GLUTAMINE-RICH ...SMALL GLUTAMINE RICH PROTEIN WITH TETRATRICOPEPTIDE REPEAT 1 / SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT (TPR)-CONTAINING / ALPHA / ISOFORM CRA_A


Mass: 14430.173 Da / Num. of mol.: 2 / Fragment: TETRATRICOPEPTIDE REPEAT, RESIDUES 84-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6FIA9, UniProt: O43765*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.7 Å3/Da / Density % sol: 54.4 % / Description: NONE
Crystal growDetails: 4M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.95
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 12726 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.8 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WAO

1wao


Resolution: 2.4→29.71 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1088998.47 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 651 5.1 %RANDOM
Rwork0.187 ---
obs0.187 12690 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7274 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.3 Å20 Å20 Å2
2--2.29 Å20 Å2
3---3.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 0 180 2137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.894
X-RAY DIFFRACTIONc_mcangle_it6.518
X-RAY DIFFRACTIONc_scbond_it10.418
X-RAY DIFFRACTIONc_scangle_it12.4612
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 99 4.8 %
Rwork0.266 1970 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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