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- PDB-1xjh: NMR structure of the redox switch domain of the E. coli Hsp33 -

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Basic information

Entry
Database: PDB / ID: 1xjh
TitleNMR structure of the redox switch domain of the E. coli Hsp33
Components33 kDa chaperonin
KeywordsCHAPERONE / REDOX-SWITCH DOMAIN / ZINC-BINDING DOMAIN / FOUR CYSTEINS COORDINATING ZINC
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
HSP33 redox switch-like / Heat shock protein Hsp33, helix hairpin bin domain superfamily / Heat shock protein Hsp33 / Heat shock protein Hsp33, N-terminal / Heat shock protein Hsp33, C-terminal / Hsp33 protein / CBS domain Like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics, molecular dynamics
AuthorsWon, H.S. / Low, L.Y. / De Guzman, R.N. / Martinez-Yamout, M.A. / Jakob, U. / Dyson, H.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The Zinc-dependent Redox Switch Domain of the Chaperone Hsp33 has a Novel Fold
Authors: Won, H.S. / Low, L.Y. / De Guzman, R.N. / Martinez-Yamout, M.A. / Jakob, U. / Dyson, H.J.
History
DepositionSep 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_software.name / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: 33 kDa chaperonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,1052
Polymers7,0401
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7039.806 Da / Num. of mol.: 1 / Fragment: C-terminal redox-switch domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hslO / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6Y5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1223D 15N-separated NOESY
132HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM protein U-15N,13C; 10mM Tris-acetate buffer; 100mM NaCl; 1mM DTT; 93% H2O, 7%D2O93% H2O/7% D2O
22mM protein U-15N; 10mM Tris-acetate buffer; 100mM NaCl; 1mM DTT; 93% H2O, 7%D2O93% H2O/7% D2O
Sample conditionsIonic strength: 10mM Tris-acetate; 100mM NaCl / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
NMRPipe2.3Delaglioprocessing
NMRView5Johnsondata analysis
CYANA1.0.5Guentertstructure solution
Amber7Caserefinement
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics
Software ordinal: 1
Details: the structures are based on a total of 960 restraints, 892 are NOE-derived distance constraints, 62 dihedral angle restraints,6 distance restraints from zinc coordination
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 20

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