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- PDB-1i7f: CRYSTAL STRUCTURE OF THE HSP33 DOMAIN WITH CONSTITUTIVE CHAPERONE... -

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Basic information

Entry
Database: PDB / ID: 1i7f
TitleCRYSTAL STRUCTURE OF THE HSP33 DOMAIN WITH CONSTITUTIVE CHAPERONE ACTIVITY
ComponentsHEAT SHOCK PROTEIN 33
KeywordsCHAPERONE / Hsp33 / redox sensitive molecular chaperone
Function / homology
Function and homology information


maintenance of unfolded protein / protein folding chaperone / unfolded protein binding / response to heat / protein refolding / response to oxidative stress / zinc ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
helix hairpin bin / Heat shock protein Hsp33, helix hairpin bin domain superfamily / Hsp33 domain / Hsp33 domain / Heat shock protein Hsp33 / Heat shock protein Hsp33, N-terminal / Heat shock protein Hsp33, C-terminal / Hsp33 protein / 3-Layer(bab) Sandwich / Helix Hairpins ...helix hairpin bin / Heat shock protein Hsp33, helix hairpin bin domain superfamily / Hsp33 domain / Hsp33 domain / Heat shock protein Hsp33 / Heat shock protein Hsp33, N-terminal / Heat shock protein Hsp33, C-terminal / Hsp33 protein / 3-Layer(bab) Sandwich / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKim, S.-J. / Jeong, D.-G. / Chi, S.-W. / Lee, J.-S. / Ryu, S.-E.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of proteolytic fragments of the redox-sensitive Hsp33 with constitutive chaperone activity
Authors: Kim, S.J. / Jeong, D.G. / Chi, S.W. / Lee, J.S. / Ryu, S.E.
History
DepositionMar 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN 33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1704
Polymers32,8851
Non-polymers2843
Water27015
1
A: HEAT SHOCK PROTEIN 33
hetero molecules

A: HEAT SHOCK PROTEIN 33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3398
Polymers65,7712
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area10920 Å2
ΔGint-103 kcal/mol
Surface area20260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.293, 77.293, 193.893
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein HEAT SHOCK PROTEIN 33


Mass: 32885.496 Da / Num. of mol.: 1 / Fragment: THE DOMAIN WITH CONSTITUTIVE CHAPERONE ACTIVITY / Mutation: C141D, C239S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HSP33 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A6Y5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116-18 mg/mlprotein1drop
227-28 %(w/v)PEG80001reservoir
30.1 MHEPES-NaOH1reservoir
40.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9879 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9879 Å / Relative weight: 1
ReflectionResolution: 2.7→99 Å / Num. all: 75273 / Num. obs: 10156 / % possible obs: 99.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.1
Reflection
*PLUS
Num. measured all: 75273
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.348

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→99 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.29 -5% of all data
Rwork0.222 --
obs-9862 -
Refinement stepCycle: LAST / Resolution: 2.7→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 16 15 1816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 99 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.222 / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09

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