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- PDB-3gl1: Crystal structure of ATPase domain of Ssb1 chaperone, a member of... -

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Basic information

Entry
Database: PDB / ID: 3gl1
TitleCrystal structure of ATPase domain of Ssb1 chaperone, a member of the HSP70 family, from Saccharomyces cerevisiae
ComponentsHeat shock protein SSB1Heat shock response
KeywordsCHAPERONE / structural genomics / APC90063.1 / ATPase domain / Ssb1 / HSP70 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / ATP-binding / Nucleotide-binding / Phosphoprotein / Protein biosynthesis / Stress response
Function / homology
Function and homology information


translational frameshifting / 'de novo' cotranslational protein folding / misfolded protein binding / : / ribosomal subunit export from nucleus / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / response to unfolded protein / regulation of translational fidelity / cellular response to unfolded protein ...translational frameshifting / 'de novo' cotranslational protein folding / misfolded protein binding / : / ribosomal subunit export from nucleus / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / response to unfolded protein / regulation of translational fidelity / cellular response to unfolded protein / cellular response to glucose starvation / translational termination / protein folding chaperone / heat shock protein binding / rRNA processing / unfolded protein binding / cytoplasmic translation / protein refolding / calmodulin binding / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily ...Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosome-associated molecular chaperone SSB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsOsipiuk, J. / Li, H. / Bargassa, M. / Sahi, C. / Craig, E.A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of ATPase domain of Ssb1 chaperone, member of the HSP70 family from Saccharomyces cerevisiae.
Authors: Osipiuk, J. / Li, H. / Bargassa, M. / Sahi, C. / Craig, E.A. / Joachimiak, A.
History
DepositionMar 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein SSB1
B: Heat shock protein SSB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,60613
Polymers84,1932
Non-polymers41311
Water12,034668
1
A: Heat shock protein SSB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2877
Polymers42,0961
Non-polymers1906
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein SSB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3196
Polymers42,0961
Non-polymers2235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.543, 54.504, 90.623
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heat shock protein SSB1 / Heat shock response / Cold-inducible protein YG101


Mass: 42096.445 Da / Num. of mol.: 2 / Fragment: UNP residues 1-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SSB1, YDL229W, YG101 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11484
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 43.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Magnesium chloride, 0.1 M Tris buffer, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.92→37.7 Å / Num. all: 54607 / Num. obs: 54607 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.982
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.11 / % possible all: 86.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YUW

1yuw


Resolution: 1.92→37.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 7.944 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21776 2773 5.1 %RANDOM
Rwork0.16408 ---
obs0.16672 54590 97.74 %-
all-54590 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.033 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å2-1.41 Å2
2---0.15 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.92→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5856 0 16 668 6540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226092
X-RAY DIFFRACTIONr_bond_other_d0.0010.024177
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9688259
X-RAY DIFFRACTIONr_angle_other_deg0.918310248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6725805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57224.672274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71151108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1611542
X-RAY DIFFRACTIONr_chiral_restr0.0990.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021202
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_it0.8561.53850
X-RAY DIFFRACTIONr_mcbond_other0.2731.51584
X-RAY DIFFRACTIONr_mcangle_it1.42826224
X-RAY DIFFRACTIONr_scbond_it2.4632242
X-RAY DIFFRACTIONr_scangle_it4.0114.52013
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 150 -
Rwork0.26 3017 -
obs--77.28 %
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)
12.07050.47470.10762.8715-0.77683.3904-0.00630.1002-0.0133-0.22760.10660.05090.0845-0.0453-0.10030.0206-0.0015-0.00930.0275-0.02440.07577.940733.423150.6032
20.9943-0.33680.01240.9190.40612.04530.0597-0.0707-0.09670.0318-0.0169-0.05890.0057-0.0047-0.04280.0156-0.01540.00520.03840.00410.05769.651132.423266.1572
31.32210.42810.55130.53810.37373.61270.0092-0.23780.02340.0392-0.18090.0723-0.2259-0.58510.17170.03450.02140.01260.1274-0.03860.03741.053536.991871.9485
41.266-0.2608-0.1640.12260.05582.2270.05890.0272-0.0138-0.0697-0.02670.0853-0.0906-0.1504-0.03230.05310.0201-0.06650.0225-0.02450.10290.116732.576451.932
55.5228-1.13222.33861.70290.63126.64410.11030.3268-0.0517-0.1913-0.06320.258-0.3119-0.0366-0.04710.06370.0139-0.08080.02590.00660.1735-6.364716.647747.4386
612.0081-2.540312.1630.5379-2.573612.3211-0.9533-1.48620.49910.21010.3774-0.1147-1.0091-1.51530.57580.2222-0.0095-0.03320.7331-0.12170.47860.062614.550366.3557
72.65120.59381.36191.44050.67731.71770.0837-0.3103-0.1340.066-0.04030.21180.1339-0.0652-0.04340.0945-0.0203-0.00010.09610.04410.122218.48377.995774.2008
86.2663-0.60894.59820.7424-0.63847.04530.1518-0.4509-0.6974-0.1509-0.01910.29070.4912-0.2831-0.13270.0917-0.0128-0.04390.04680.04820.2249-8.8096.429958.0157
93.32820.83381.57521.41130.12143.5123-0.14110.146-0.1829-0.18760.0084-0.0713-0.01920.1690.13270.05490.0073-0.04780.0133-0.01920.14812.94798.733952.8199
100.78470.15940.374.145-0.81910.36940.13630.0638-0.1911-0.2844-0.0486-0.04450.12830.044-0.08770.06260.0216-0.03860.0196-0.03990.09233.419914.252948.7188
111.80840.2840.06492.21691.00437.88670.0834-0.31320.2170.0735-0.0880.1726-0.0888-0.18960.00460.0166-0.015-0.00340.1074-0.05230.087834.627935.588880.5389
124.8086-2.24544.22132.87470.207214.0738-0.178-0.6263-0.28340.61530.15890.2302-0.2160.03730.01910.2255-0.07580.0060.1868-0.02430.226826.86432.713883.2131
130.74060.353-0.12513.4918-2.85233.2312-0.0004-0.06260.13-0.00740.03890.2727-0.1358-0.1516-0.03850.02920.0239-0.03990.0384-0.04250.094829.590140.107665.7394
140.59710.19370.06280.8307-0.36391.66510.0067-0.06340.118-0.0814-0.0704-0.0021-0.05360.11220.06370.03010.0031-0.01720.025-0.01880.058442.167139.58668.8965
150.70630.14110.84020.8125-0.34575.5540.0472-0.1780.0080.0753-0.0596-0.0816-0.0808-0.17240.01240.0201-0.0176-0.01980.08870.00830.032246.839519.848183.597
161.22510.2641.95410.210.49063.43010.02890.0699-0.0114-0.016-0.0483-0.06450.03250.09580.01940.04850.0118-0.00110.05670.01640.047442.363219.668964.7307
170.549-0.4025-0.26859.22686.96638.90770.15450.08940.2388-0.6204-0.1003-0.0059-0.5605-0.3445-0.05420.07340.03750.05990.07240.06820.124929.129423.509544.5775
181.25241.0436-0.66022.4451-2.63453.21090.10040.0556-0.01260.09450.03080.0544-0.0523-0.0438-0.13120.06750.0245-0.00620.0368-0.00320.044327.144917.001959.9797
192.9186-1.05773.34634.037-4.31016.50680.14220.0435-0.0891-0.20170.03320.14480.2984-0.0294-0.17530.07430.0316-0.00440.0497-0.01890.021225.541114.050550.9575
200.74070.64150.68011.18630.48670.67750.1637-0.0762-0.09280.1063-0.11-0.02410.1775-0.0467-0.05370.06030.01470.00190.06450.02420.058843.490414.582976.2803
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 24
2X-RAY DIFFRACTION2A25 - 80
3X-RAY DIFFRACTION3A81 - 132
4X-RAY DIFFRACTION4A133 - 188
5X-RAY DIFFRACTION5A189 - 224
6X-RAY DIFFRACTION6A225 - 236
7X-RAY DIFFRACTION7A237 - 311
8X-RAY DIFFRACTION8A312 - 331
9X-RAY DIFFRACTION9A332 - 350
10X-RAY DIFFRACTION10A351 - 384
11X-RAY DIFFRACTION11B4 - 24
12X-RAY DIFFRACTION12B25 - 34
13X-RAY DIFFRACTION13B35 - 53
14X-RAY DIFFRACTION14B54 - 186
15X-RAY DIFFRACTION15B187 - 211
16X-RAY DIFFRACTION16B212 - 250
17X-RAY DIFFRACTION17B251 - 264
18X-RAY DIFFRACTION18B265 - 284
19X-RAY DIFFRACTION19B285 - 305
20X-RAY DIFFRACTION20B306 - 384

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