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- PDB-3sz7: Crystal structure of the Sgt2 TPR domain from Aspergillus fumigatus -

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Basic information

Entry
Database: PDB / ID: 3sz7
TitleCrystal structure of the Sgt2 TPR domain from Aspergillus fumigatus
ComponentsHsc70 cochaperone (SGT)
KeywordsCHAPERONE REGULATOR / TPR domain / Cochaperone / Get4 / Get5 / Get3 / Mdy2 / Ssa1 / Sse1 / Hsp104 / Hsc82
Function / homology
Function and homology information


TRC complex / post-translational protein targeting to endoplasmic reticulum membrane / protein serine/threonine phosphatase activity / response to heat / molecular adaptor activity / identical protein binding / membrane
Similarity search - Function
SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat profile. / Tetratricopeptide repeats ...SGTA, homodimerisation domain / Homodimerisation domain of SGTA / : / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / TPR repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / 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
Heat-shock protein cognate (HSC) co-chaperone sgt12
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsChartron, J.W. / Gonzalez, G.M. / Clemons Jr., W.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: A structural model of the Sgt2 protein and its interactions with chaperones and the Get4/Get5 complex.
Authors: Chartron, J.W. / Gonzalez, G.M. / Clemons, W.M.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Sep 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 / 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

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Assembly

Deposited unit
A: Hsc70 cochaperone (SGT)


Theoretical massNumber of molelcules
Total (without water)17,2681
Polymers17,2681
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hsc70 cochaperone (SGT)

A: Hsc70 cochaperone (SGT)


Theoretical massNumber of molelcules
Total (without water)34,5362
Polymers34,5362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4220 Å2
ΔGint-6 kcal/mol
Surface area14670 Å2
MethodPISA
3
A: Hsc70 cochaperone (SGT)

A: Hsc70 cochaperone (SGT)


Theoretical massNumber of molelcules
Total (without water)34,5362
Polymers34,5362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
Buried area1400 Å2
ΔGint-11 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.610, 86.770, 116.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-15-

HOH

21A-21-

HOH

31A-32-

HOH

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Components

#1: Protein Hsc70 cochaperone (SGT)


Mass: 17268.113 Da / Num. of mol.: 1 / Fragment: UNP residues 109-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_1G09830 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4WTC0, protein-serine/threonine phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 25% PEG 1500, 0.1M MES, Malic acid, Tris, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2010
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: 1.72→26.535 Å / Num. all: 15756 / Num. obs: 15756 / % possible obs: 97.2 % / Redundancy: 4 % / Rsym value: 0.06 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.72-1.814.10.5021.2947123160.50298.8
1.81-1.9240.3072.1861121760.30799
1.92-2.063.60.1853.5710519620.18594.2
2.06-2.224.30.1215.5830119200.12198.9
2.22-2.434.20.097.4743717800.0998.8
2.43-2.7240.06510643816000.06598
2.72-3.143.90.04912.9521513470.04993.3
3.14-3.854.30.03915.7521412050.03998.1
3.85-5.443.90.03318.235279080.03393.6
5.44-26.5354.30.03119.223215420.03196.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2VYI

2vyi


Resolution: 1.72→25.397 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 0 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 1524 10.05 %Random
Rwork0.169 ---
obs0.173 15169 93.32 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.22 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 91.2 Å2 / Biso mean: 27.115 Å2 / Biso min: 8.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.9518 Å2-0 Å2-0 Å2
2---3.2148 Å20 Å2
3----0.737 Å2
Refinement stepCycle: LAST / Resolution: 1.72→25.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 0 109 1233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041142
X-RAY DIFFRACTIONf_angle_d0.7431537
X-RAY DIFFRACTIONf_chiral_restr0.048159
X-RAY DIFFRACTIONf_plane_restr0.003209
X-RAY DIFFRACTIONf_dihedral_angle_d11.168436
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.77550.31061310.25461142127387
1.7755-1.8390.23031320.21851179131190
1.839-1.91260.27691410.21021201134291
1.9126-1.99960.26291280.19571162129089
1.9996-2.1050.2241360.16841232136893
2.105-2.23680.19941400.14781274141497
2.2368-2.40930.19761460.15391309145598
2.4093-2.65160.19971390.15491280141997
2.6516-3.03470.18151370.15431228136591
3.0347-3.82130.18131460.15351311145798
3.8213-25.39930.21181480.17741327147594
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0049-0.40250.64041.8712-0.4060.3820.05370.6798-0.26190.0485-0.31950.10130.56550.1184-0.00180.50430.1254-0.07370.2719-0.07310.246233.21259.560726.7457
20.36530.21860.06080.22210.13660.14480.1328-0.0806-0.5689-0.15480.08620.00920.63280.0954-0.03570.51390.1441-0.12190.1744-0.03640.310234.66619.802743.5006
30.81640.0208-0.32421.03260.68071.14130.03790.0446-0.0958-0.02050.1547-0.18150.23810.2898-0.00990.1630.0606-0.02790.1637-0.04790.147634.192921.260240.9384
40.7164-0.41290.49520.39460.03320.46580.00930.0699-0.1245-0.0090.0668-0.0510.02220.2091-0.04890.08270.0011-0.01790.129-0.02140.105827.692531.255345.0704
50.7187-0.29250.18560.7776-0.53770.79210.00830.09630.196-0.12590.11950.3775-0.0002-0.0448-0.03130.1042-0.0292-0.02040.11780.00760.160118.651332.278844.3777
60.6983-0.04880.64410.91150.13270.67790.1085-0.025-0.02660.3204-0.0967-0.07580.0444-0.2409-0.00150.1164-0.00420.00460.15760.00620.09820.461538.946553.2163
70.4391-0.1550.13460.2545-0.0770.02920.13060.00240.0017-0.03-0.15090.0672-0.8419-0.20210.00120.48860.06350.01780.1729-0.04080.237724.966166.654969.911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 104:111)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 112:126)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 127:181)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 182:197)A0
5X-RAY DIFFRACTION5chain 'A' and (resseq 198:217)A0
6X-RAY DIFFRACTION6chain 'A' and (resseq 218:236)A0
7X-RAY DIFFRACTION7chain 'A' and (resseq 237:254)A0

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