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- PDB-5v47: Crystal structure of the SR1 domain of lizard sacsin -

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Basic information

Entry
Database: PDB / ID: 5v47
TitleCrystal structure of the SR1 domain of lizard sacsin
ComponentsLizard sacsin
KeywordsCHAPERONE / alpha-beta sandwich / Bergerat fold
Function / homology
Function and homology information


negative regulation of inclusion body assembly / proteasome binding / Hsp70 protein binding / protein-folding chaperone binding / mitochondrion / nucleus
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 / Ubiquitin homologues ...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 homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesAnolis carolinensis (green anole)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsPan, T. / Menade, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lizard sacsin
B: Lizard sacsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5983
Polymers57,5022
Non-polymers961
Water4,540252
1
A: Lizard sacsin


Theoretical massNumber of molelcules
Total (without water)28,7511
Polymers28,7511
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lizard sacsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8472
Polymers28,7511
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.779, 38.164, 114.721
Angle α, β, γ (deg.)90.00, 131.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lizard sacsin


Mass: 28751.053 Da / Num. of mol.: 2 / Fragment: UNP residues 96-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anolis carolinensis (green anole) / Gene: SACS / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: G1KBF9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M lithium sulfate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 43261 / % possible obs: 99.29 % / Redundancy: 3.7 % / Rsym value: 0.114 / Net I/σ(I): 20.4
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2962 / Rsym value: 0.567 / % possible all: 91.76

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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: 1.84→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.069 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.133
RfactorNum. reflection% reflectionSelection details
Rfree0.23401 2284 5 %RANDOM
Rwork0.19526 ---
obs0.19732 43261 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.149 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.21 Å2
2---0.16 Å20 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3721 0 5 252 3978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193822
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.945181
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_restr0.0940.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213011
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_it0.9541.4771840
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5392.2062293
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3821.6571982
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.20115.6835088
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: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 145 -
Rwork0.252 2962 -
obs--91.76 %
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)
17.0922.15644.42580.65861.34192.7691-0.13070.27920.1206-0.03780.08730.0573-0.08910.18660.04340.034-0.07780.01150.19860.02720.148545.015327.203520.5958
22.1199-1.4124-0.84322.96330.94612.37920.1390.04970.1102-0.1325-0.0374-0.2437-0.0484-0.0193-0.10150.0882-0.0231-0.0060.07950.03270.131524.677714.340516.1906
31.86980.6001-0.64972.0029-0.82452.3220.0133-0.1966-0.07550.0945-0.0606-0.2172-0.01040.18120.04740.0616-0.0144-0.02090.08420.04170.08326.167214.702726.0768
41.54680.43940.23283.008-0.35821.8625-0.04740.14360.1385-0.22440.07650.07230.0117-0.0516-0.02910.07680.0007-0.00290.10470.03650.100723.805918.224214.4464
55.685-4.1021-3.200610.4487-2.99787.88650.37060.65410.1815-0.6788-0.4089-0.6318-0.19440.1570.03830.1620.00940.06260.2449-0.02550.070731.70765.15790.6861
611.1899-7.1484-7.03714.88445.37037.14960.29550.9193-0.4904-0.0795-0.54770.28980.191-0.5640.25220.11620.0405-0.04140.165-0.0330.045916.452110.84594.5712
713.50052.734-3.37730.9867-0.63610.8549-0.18251.05650.0358-0.26540.2195-0.06570.0275-0.2797-0.03690.1367-0.033-0.00390.1860.00090.1706-28.98982.210820.7704
85.72981.1843-0.207612.90873.94936.49150.34730.2632-0.4183-0.2575-0.44370.14050.0061-0.86060.09640.05660.0383-0.03710.22330.01730.0754-16.875721.189414.4798
91.0922-0.1771-0.28721.61280.27791.7556-0.0177-0.0467-0.02180.1239-0.02470.15170.0764-0.09850.04240.0694-0.0074-0.00210.0351-0.00950.0769-13.03115.583331.4479
101.17970.1516-0.10453.13980.57050.6702-0.02180.0777-0.1144-0.26280.0547-0.1275-0.0470.0367-0.03290.1134-0.0041-0.00720.0655-0.01010.0862-8.750112.99922.1525
1117.9585-6.4262-7.143919.27384.95473.1829-0.16790.9039-0.5790.0659-0.07160.28670.0539-0.34940.23950.33780.0646-0.05650.3820.02420.044-14.721624.40784.1995
126.9042-2.78821.39961.1624-0.87233.4590.13470.38080.3223-0.0053-0.1262-0.1104-0.5547-0.002-0.00850.1206-0.00020.00280.0760.05970.0797-1.468221.587414.8743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A95 - 115
2X-RAY DIFFRACTION2A116 - 173
3X-RAY DIFFRACTION3A174 - 265
4X-RAY DIFFRACTION4A266 - 305
5X-RAY DIFFRACTION5A306 - 323
6X-RAY DIFFRACTION6A324 - 342
7X-RAY DIFFRACTION7B96 - 116
8X-RAY DIFFRACTION8B117 - 135
9X-RAY DIFFRACTION9B136 - 264
10X-RAY DIFFRACTION10B265 - 308
11X-RAY DIFFRACTION11B309 - 318
12X-RAY DIFFRACTION12B319 - 342

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