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- PDB-3m7m: Crystal structure of monomeric hsp33 -

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Basic information

Entry
Database: PDB / ID: 3m7m
TitleCrystal structure of monomeric hsp33
Components33 kDa chaperonin
KeywordsCHAPERONE / alpha/beta structure / Disulfide bond / Redox-active center / Stress response
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChi, S.W. / Jeong, D.G. / Woo, J.R. / Park, B.C. / Ryu, S.E. / Kim, S.J.
CitationJournal: To be Published
Title: Crystal structure of monomeric hsp33
Authors: Chi, S.-W. / Jeong, D.G. / Ryu, S.E. / Kim, S.J. / Woo, J.R. / Park, B.C.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: 33 kDa chaperonin


Theoretical massNumber of molelcules
Total (without water)26,1961
Polymers26,1961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.981, 65.981, 145.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 33 kDa chaperonin / Heat shock protein 33 / HSP33


Mass: 26196.412 Da / Num. of mol.: 1 / Fragment: UNP residues 1-233 / Mutation: C141D, Q151E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6Y5
Sequence detailsAUTHOR STATED THAT THE N-TERMINAL MET AND ILE WERE THE REAL SEQUENCE IN E.COLI HSP33.

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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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: May 11, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 7120 / Num. obs: 6752 / % possible obs: 91.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 11.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1i7F

1i7f


Resolution: 2.9→30.06 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.869 / SU B: 21.248 / SU ML: 0.375 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28059 326 4.6 %RANDOM
Rwork0.2242 ---
obs0.22673 6752 92.35 %-
all-7120 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 70.315 Å2
Baniso -1Baniso -2Baniso -3
1-5.28 Å20 Å20 Å2
2--5.28 Å20 Å2
3----10.56 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 0 1810
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.018
X-RAY DIFFRACTIONr_angle_refined_deg2.85
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.782
X-RAY DIFFRACTIONr_chiral_restr0.125
X-RAY DIFFRACTIONr_gen_planes_refined0.026
X-RAY DIFFRACTIONr_nbd_refined0.34
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.208
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.421
X-RAY DIFFRACTIONr_mcbond_it3.658
X-RAY DIFFRACTIONr_mcangle_it6.254
X-RAY DIFFRACTIONr_scbond_it7.541
X-RAY DIFFRACTIONr_scangle_it11.435
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.554 17
Rwork0.364 399
Refinement TLS params.Method: refined / Origin x: 60.2462 Å / Origin y: 25.2366 Å / Origin z: 16.8831 Å
111213212223313233
T0.0483 Å20.0192 Å20.0137 Å2-0.1519 Å20.0212 Å2--0.3048 Å2
L1.3746 °20.5751 °20.6423 °2-1.6881 °2-0.4282 °2--5.5576 °2
S0.0119 Å °0.1848 Å °-0.0342 Å °-0.0589 Å °0.0719 Å °-0.0934 Å °0.0526 Å °0.2267 Å °-0.0839 Å °

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