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- PDB-5v46: Crystal structure of the I113M, F270M, K291M, L308M mutant of SR1... -

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Basic information

Entry
Database: PDB / ID: 5v46
TitleCrystal structure of the I113M, F270M, K291M, L308M mutant of SR1 domain of human sacsin
ComponentsSacsin
KeywordsCHAPERONE / alpha-beta sandwich / Bergerat fold
Function / homology
Function and homology information


negative regulation of inclusion body assembly / cell body fiber / low-density lipoprotein particle receptor binding / proteasome binding / Hsp70 protein binding / protein folding / protein-folding chaperone binding / axon / dendrite / mitochondrion ...negative regulation of inclusion body assembly / cell body fiber / low-density lipoprotein particle receptor binding / proteasome binding / Hsp70 protein binding / protein folding / protein-folding chaperone binding / axon / dendrite / mitochondrion / identical protein binding / nucleus / cytoplasm
Similarity search - Function
: / HEPN domain profile. / Higher Eukarytoes and Prokaryotes Nucleotide-binding domain / HEPN domain / HEPN domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Histidine kinase/HSP90-like ATPase superfamily / Ubiquitin family ...: / HEPN domain profile. / Higher Eukarytoes and Prokaryotes Nucleotide-binding domain / HEPN domain / HEPN domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Histidine kinase/HSP90-like ATPase superfamily / Ubiquitin family / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMenade, M. / Kozlov, G. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
ARSACS Foundation Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structures of ubiquitin-like (Ubl) and Hsp90-like domains of sacsin provide insight into pathological mutations.
Authors: Menade, M. / Kozlov, G. / Trempe, J.F. / Pande, H. / Shenker, S. / Wickremasinghe, S. / Li, X. / Hojjat, H. / Dicaire, M.J. / Brais, B. / McPherson, P.S. / Wong, M.J.H. / Young, J.C. / Gehring, K.
History
DepositionMar 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 4, 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sacsin
B: Sacsin


Theoretical massNumber of molelcules
Total (without water)57,6932
Polymers57,6932
Non-polymers00
Water3,657203
1
A: Sacsin


Theoretical massNumber of molelcules
Total (without water)28,8461
Polymers28,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sacsin


Theoretical massNumber of molelcules
Total (without water)28,8461
Polymers28,8461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.753, 70.753, 100.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Sacsin / DnaJ homolog subfamily C member 29 / DNAJC29


Mass: 28846.482 Da / Num. of mol.: 2 / Fragment: UNP residues 89-336 / Mutation: I113M,F270M,K291M,L308M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SACS, KIAA0730 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9NZJ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 28% PEG 3350, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 43323 / % possible obs: 99.9 % / Redundancy: 15.2 % / Rsym value: 0.096 / Net I/σ(I): 47
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 15 % / Mean I/σ(I) obs: 6.4 / Rsym value: 0.592 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V45

5v45


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.532 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2299 5 %RANDOM
Rwork0.198 ---
obs0.2 43323 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 0 203 4143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194052
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9675490
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
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_restr0.0950.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213147
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6041.0421976
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9631.5582464
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1051.1992076
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.78211.3195141
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: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 176 -
Rwork0.218 3155 -
obs--99.37 %
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)
15.4284-2.3079-2.75571.1190.77252.6180.19960.14530.6904-0.1094-0.0418-0.37140.0256-0.0761-0.15780.06360.01620.02010.0819-0.03120.16442.067628.862282.6047
26.67526.40026.46167.04143.922811.98740.3477-0.2192-0.07960.4813-0.3841-0.1514-0.05680.21530.03650.22780.02060.01660.2602-0.0890.321731.903821.763894.7055
30.6595-0.0562-0.47471.07230.10511.1518-0.0167-0.01810.0202-0.0186-0.00140.0706-0.0104-0.04880.01810.0109-0.00020.00170.0411-0.00930.070624.09518.361779.1692
41.8185-0.13241.6180.0108-0.11161.4802-0.4292-0.15330.51940.0040.0047-0.0545-0.5709-0.17670.42440.99010.2218-0.02370.07980.05170.81932.068345.838684.0613
50.98710.1578-0.45730.96290.29010.9661-0.00380.0450.1084-0.04350.0129-0.0183-0.1142-0.0234-0.00910.0323-0.00940.01080.0381-0.0030.067628.719226.187377.2329
61.2824-0.1705-0.07421.2916-0.39021.1528-0.0353-0.034-0.044-0.05740.04730.01150.0857-0.0958-0.0120.0492-0.00530.01640.0634-0.02430.070825.929214.094875.9139
72.3591-1.447-1.60031.40631.98243.7472-0.1517-0.1369-0.1370.24590.03190.10380.3624-0.12180.11980.0754-0.00020.05170.03140.01010.079618.98377.950791.6654
810.3044-2.06814.08115.93850.09988.7742-0.02440.21850.2998-0.10670.0831-0.1738-0.06710.2376-0.05870.07420.00520.04260.02490.02730.098964.97892.352475.7196
91.1436-0.0618-0.09230.71510.27181.07660.0821-0.0254-0.0743-0.0758-0.0742-0.03290.08730.0088-0.00790.064-0.00040.01310.013-0.00030.056552.9655-9.47983.582
100.2925-0.11661.7770.0467-0.711910.9072-0.09850.17250.04450.0416-0.0766-0.0205-0.53351.27440.17510.3006-0.0001-0.17180.5943-0.14980.664480.7266-1.992579.4728
111.42740.1084-0.43240.76860.29991.27320.095-0.1760.00080.0685-0.0587-0.05640.08060.1219-0.03630.0672-0.01720.00550.03640.00970.04460.3201-7.627289.1079
121.404-0.04640.20131.4174-0.04211.07160.0786-0.13780.01180.0557-0.05080.02470.1165-0.0821-0.02780.0534-0.02360.0270.0391-0.01370.065948.4811-6.921187.8367
134.0234-5.4601-4.919710.79876.81926.03380.01680.4279-0.0472-0.3502-0.1001-0.12380.0121-0.49740.08330.28620.01250.02710.1658-0.03530.131445.3473-11.414765.5792
144.118-2.5662-3.73234.34312.53245.17320.10310.167-0.3954-0.1744-0.10330.51090.2233-0.37110.00020.0974-0.0438-0.07440.071-0.00260.176639.36-14.039476.4847
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 105
2X-RAY DIFFRACTION2A106 - 113
3X-RAY DIFFRACTION3A114 - 177
4X-RAY DIFFRACTION4A178 - 184
5X-RAY DIFFRACTION5A185 - 231
6X-RAY DIFFRACTION6A232 - 300
7X-RAY DIFFRACTION7A301 - 336
8X-RAY DIFFRACTION8B93 - 107
9X-RAY DIFFRACTION9B108 - 177
10X-RAY DIFFRACTION10B178 - 184
11X-RAY DIFFRACTION11B185 - 241
12X-RAY DIFFRACTION12B242 - 294
13X-RAY DIFFRACTION13B295 - 310
14X-RAY DIFFRACTION14B311 - 335

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