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- PDB-1hw7: HSP33, HEAT SHOCK PROTEIN WITH REDOX-REGULATED CHAPERONE ACTIVITY -

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Basic information

Entry
Database: PDB / ID: 1hw7
TitleHSP33, HEAT SHOCK PROTEIN WITH REDOX-REGULATED CHAPERONE ACTIVITY
ComponentsHEAT SHOCK PROTEIN HSP33
KeywordsCHAPERONE / Hsp33 / dimerization / heat shock protein / oxidative stress
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 / cytoplasm / cytosol
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: 2.2 Å
AuthorsVijayalakshmi, J. / Mukhergee, M.K. / Graumann, J. / Jakob, U. / Saper, M.A.
CitationJournal: Structure / Year: 2001
Title: The 2.2 A crystal structure of Hsp33: a heat shock protein with redox-regulated chaperone activity.
Authors: Vijayalakshmi, J. / Mukhergee, M.K. / Graumann, J. / Jakob, U. / Saper, M.A.
History
DepositionJan 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEAT SHOCK PROTEIN HSP33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0877
Polymers28,4421
Non-polymers6456
Water2,594144
1
A: HEAT SHOCK PROTEIN HSP33
hetero molecules

A: HEAT SHOCK PROTEIN HSP33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,17414
Polymers56,8842
Non-polymers1,29012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area12810 Å2
ΔGint-211 kcal/mol
Surface area19700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.180, 77.180, 199.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe second part of the biological assembly is generated by the two fold axis: -Y, -X, -Z+1/6 applied to chain A

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Components

#1: Protein HEAT SHOCK PROTEIN HSP33 / 33 KDA CHAPERONIN


Mass: 28442.018 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HSLO / Plasmid: PET11A(PSS1) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.12 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Drops contained 2 microlitres of protein solution (10mg/ml in 20mM KCL, 40mM HEPES pH 7.5) supplemented with 2mM DTT and 0.3 mM ZnCl2 and 2 microlitres of precipitant (1.5 M ammonium ...Details: Drops contained 2 microlitres of protein solution (10mg/ml in 20mM KCL, 40mM HEPES pH 7.5) supplemented with 2mM DTT and 0.3 mM ZnCl2 and 2 microlitres of precipitant (1.5 M ammonium sulfate, 10% dioxane, 0.1 M MES pH 6.8) and were equilibrated against 1ml of the same precipitant., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mM1dropKCl
340 mMHEPES1drop
420 mMdithiothreitol1drop
51.5 Mammonium sulfate1reservoir
610 %dioxane1reservoir
70.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2000 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent cylindrical Ge(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 18629 / Num. obs: 18629 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 23.9 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 45.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 14 / Num. unique all: 1968 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 444763
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: Structure phased by three-wavelength MAD experiment of AUCN-derived crystals and refined to 2.4 A.

Resolution: 2.2→30 Å / Cross valid method: Free R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used Bijovoet pairs of reflections, anomalous corrections to scattering factors for Zn at 1A and bulk solvent corrections
RfactorNum. reflection% reflectionSelection details
Rfree0.2567 1671 5 %RANDOM
Rwork0.2295 ---
all-33455 --
obs-33455 99.3 %-
Solvent computationBsol: 77.4 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 33 144 1966
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_mcbond_it2.81.5
X-RAY DIFFRACTIONc_mcangle_it4.32
X-RAY DIFFRACTIONc_scbond_it4.12
X-RAY DIFFRACTIONc_scangle_it5.82.5
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it2.81.5
X-RAY DIFFRACTIONc_scbond_it4.12
X-RAY DIFFRACTIONc_mcangle_it4.32
X-RAY DIFFRACTIONc_scangle_it5.82.5

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