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- PDB-1vzy: Crystal structure of the Bacillus subtilis HSP33 -

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Basic information

Entry
Database: PDB / ID: 1vzy
TitleCrystal structure of the Bacillus subtilis HSP33
Components33 KDA CHAPERONIN
KeywordsCHAPERONE / HEAT SHOCK PROTEIN / CRYSTAL ENGINEERING / MOLECULAR CHAPERONE / REDOX-ACTIVE CENTER / PSI / PROTEIN STRUCTURE INITIATIVE / MCSG / MIDWEST CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


protein folding chaperone / unfolded protein binding / protein refolding / cytoplasm
Similarity search - Function
HSP33 redox switch-like / Hsp33 domain / Hsp33 domain / Heat shock protein Hsp33 / Heat shock protein Hsp33, N-terminal / Heat shock protein Hsp33, C-terminal / Hsp33 protein / CBS domain Like / 3-Layer(bab) Sandwich / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 33 kDa chaperonin
Similarity search - Component
Biological speciesBacillus subtilis 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.97 Å
AuthorsJanda, I.K. / Devedjiev, Y. / Derewenda, U. / Dauter, Z. / Bielnicki, J. / Cooper, D.R. / Joachimiak, A. / Derewenda, Z.S. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Structure / Year: 2004
Title: The crystal structure of the reduced, Zn2+-bound form of the B. subtilis Hsp33 chaperone and its implications for the activation mechanism.
Authors: Janda, I. / Devedjiev, Y. / Derewenda, U. / Dauter, Z. / Bielnicki, J. / Cooper, D.R. / Graf, P.C. / Joachimiak, A. / Jakob, U. / Derewenda, Z.S.
History
DepositionMay 29, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2004Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 1.3May 8, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 33 KDA CHAPERONIN
B: 33 KDA CHAPERONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,94710
Polymers63,4622
Non-polymers4858
Water4,990277
1
A: 33 KDA CHAPERONIN
B: 33 KDA CHAPERONIN
hetero molecules

A: 33 KDA CHAPERONIN
B: 33 KDA CHAPERONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,89520
Polymers126,9244
Non-polymers97016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)115.292, 115.292, 106.441
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 31731.084 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ZN ATOMS, MUTATION E100A AND Q101A / Source: (gene. exp.) Bacillus subtilis 168 (bacteria) / Plasmid: PMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37565
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION GLU 100 ALA AND GLN 101 ALA IN CHAINS A AND B. REDOX REGULATED MOLECULAR ...ENGINEERED MUTATION GLU 100 ALA AND GLN 101 ALA IN CHAINS A AND B. REDOX REGULATED MOLECULAR CHAPERONE. PROTECTS BOTH THERMALLY UNFOLDING AND OXIDATIVELY DAMAGED PROTEINS FROM IRREVERSIBLE AGGREGATION. PLAYS AN IMPORTANT ROLE IN THE BACTERIAL DEFENSE SYSTEM.

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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: 3.2 Å3/Da / Density % sol: 61.4 %
Crystal growpH: 7.5 / Details: 1.6 M K/NA TARTRATE, 0.1 M HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.28310,1.2837
DetectorDate: Feb 14, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28311
21.28371
ReflectionResolution: 1.97→50 Å / Num. obs: 124827 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.57
Reflection shellResolution: 1.97→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.64 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 1.97→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.766 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGION IN MOLECULE B (FROM GLY 252 - GLY 264) WAS MODELED BASED ON CORRSEPONDING FRAGMENT IN MOLECULE A, AND OCCUPANCIES WERE SET TO 0.01.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1186 2.1 %RANDOM
Rwork0.197 ---
obs-56615 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 34.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.34 Å20 Å2
2--0.69 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4382 0 26 277 4685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0214464
X-RAY DIFFRACTIONr_bond_other_d0.0020.024141
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9816026
X-RAY DIFFRACTIONr_angle_other_deg0.91339653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1190.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024991
X-RAY DIFFRACTIONr_gen_planes_other0.010.02824
X-RAY DIFFRACTIONr_nbd_refined0.2190.2869
X-RAY DIFFRACTIONr_nbd_other0.2550.24701
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.22706
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6190.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3010.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6510.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3351.52860
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2624578
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2131604
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0194.51448
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.257 72
Rwork0.203 4121

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