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- PDB-1c3g: S. CEREVISIAE HEAT SHOCK PROTEIN 40 SIS1 -

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Basic information

Entry
Database: PDB / ID: 1c3g
TitleS. CEREVISIAE HEAT SHOCK PROTEIN 40 SIS1
ComponentsHEAT SHOCK PROTEIN 40
KeywordsCHAPERONE / BETA SHEETS / SHORT HELICES
Function / homology
Function and homology information


detection of misfolded protein / tRNA import into nucleus / misfolded protein transport / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / chaperone cofactor-dependent protein refolding / cellular response to starvation / translational initiation / unfolded protein binding ...detection of misfolded protein / tRNA import into nucleus / misfolded protein transport / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / misfolded protein binding / chaperone cofactor-dependent protein refolding / cellular response to starvation / translational initiation / unfolded protein binding / protein folding / protein-folding chaperone binding / cellular response to heat / cytosolic small ribosomal subunit / nucleolus / DNA binding / nucleus / cytosol
Similarity search - Function
Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / : / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain ...Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / : / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsSha, B. / Lee, S. / Cyr, D.
CitationJournal: Structure / Year: 2000
Title: The crystal structure of the peptide-binding fragment from the yeast Hsp40 protein Sis1.
Authors: Sha, B. / Lee, S. / Cyr, D.M.
History
DepositionJul 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: HEAT SHOCK PROTEIN 40


Theoretical massNumber of molelcules
Total (without water)19,0981
Polymers19,0981
Non-polymers00
Water59433
1
A: HEAT SHOCK PROTEIN 40

A: HEAT SHOCK PROTEIN 40


Theoretical massNumber of molelcules
Total (without water)38,1962
Polymers38,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z+1/41
Unit cell
Length a, b, c (Å)73.420, 73.420, 80.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsthe biological assembly is a homodimer constructed by a crystallographic 2-fold.

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Components

#1: Protein HEAT SHOCK PROTEIN 40


Mass: 19097.801 Da / Num. of mol.: 1 / Fragment: SIS1 C-TERMINAL PEPTIDE-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: MOLECULAR CHAPERONE
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET9D / Production host: Escherichia coli (E. coli) / References: UniProt: P25294
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 3350 20%, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 25K
Crystal grow
*PLUS
Details: Sha, B.D., (1999) Acta Crystallogr, D55, 1234.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMphosphate1droppH7.2
3150 mM1dropNaCl
4100 mMphosphate1reservoirpH8.15
515 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 6400 / Num. obs: 6347 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.5
Reflection shellResolution: 2.7→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.35 / Num. unique all: 6347 / % possible all: 98
Reflection
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 6.17

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Processing

Software
NameClassification
MADSYSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Simulated annealing
RfactorNum. reflection% reflectionSelection details
Rfree0.311 502 -random
Rwork0.265 ---
all0.265 6347 --
obs0.265 6347 97 %-
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 0 33 1379
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTION1.367
X-RAY DIFFRACTIONc_angle_deg
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection Rfree: 508 / Rfactor obs: 0.265 / Rfactor Rfree: 0.311 / Rfactor Rwork: 0.265
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.367
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.613
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.291
LS refinement shell
*PLUS
Rfactor Rfree: 0.42 / Rfactor Rwork: 0.382

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