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- PDB-5tky: Crystal structure of the co-translational Hsp70 chaperone Ssb in ... -

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Basic information

Entry
Database: PDB / ID: 5tky
TitleCrystal structure of the co-translational Hsp70 chaperone Ssb in the ATP-bound, open conformation
ComponentsPutative uncharacterized protein
KeywordsCHAPERONE / Hsp70 / ribosome / translation
Function / homology
Function and homology information


non-chaperonin molecular chaperone ATPase / ATP-dependent protein folding chaperone / translation / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #10 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / 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 / Up-down Bundle / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Ribosome-associated molecular chaperone SSB1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGumiero, A. / Gese, G.V. / Weyer, F.A. / Lapouge, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Nat Commun / Year: 2016
Title: Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain.
Authors: Gumiero, A. / Conz, C. / Gese, G.V. / Zhang, Y. / Weyer, F.A. / Lapouge, K. / Kappes, J. / von Plehwe, U. / Schermann, G. / Fitzke, E. / Wolfle, T. / Fischer, T. / Rospert, S. / Sinning, I.
History
DepositionOct 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jan 17, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,9216
Polymers135,8582
Non-polymers1,0634
Water1,54986
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-25 kcal/mol
Surface area51550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.930, 128.240, 79.680
Angle α, β, γ (deg.)90.00, 93.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein


Mass: 67929.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0058460 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SCU5
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350, 0.2 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.6→46.43 Å / Num. obs: 124469 / % possible obs: 98 % / Redundancy: 3.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1034 / Net I/σ(I): 8.65
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 0.91 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4b9q

4b9q


Resolution: 2.6→46.43 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.54
RfactorNum. reflection% reflection
Rfree0.264 1976 4.88 %
Rwork0.2279 --
obs0.2297 40587 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9097 0 64 86 9247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029312
X-RAY DIFFRACTIONf_angle_d0.54212584
X-RAY DIFFRACTIONf_dihedral_angle_d15.9715718
X-RAY DIFFRACTIONf_chiral_restr0.0431466
X-RAY DIFFRACTIONf_plane_restr0.0031629
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6-2.66510.3771390.3792756408599
2.6651-2.73710.39041450.3651276599
2.7371-2.81760.34341280.3423277099
2.8176-2.90860.38581520.3207276199
2.9086-3.01250.31661370.2971274698
3.0125-3.13310.31121430.3003275099
3.1331-3.27570.34711370.2931276598
3.2757-3.44830.32111420.2529276498
3.4483-3.66430.28981410.2299271797
3.6643-3.94710.28021430.2132271597
3.9471-4.34410.22211430.1899272598
4.3441-4.97220.18681390.1747276598
4.9722-6.26230.25271440.1978276798
6.2623-48.70970.18821430.177276597

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