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- PDB-1izy: Crystal structure of Hsp31 -

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Basic information

Entry
Database: PDB / ID: 1izy
TitleCrystal structure of Hsp31
ComponentsHsp31
Keywordschaperone / hydrolase / alpha-beta sandwitch
Function / homology
Function and homology information


D-lactate dehydratase / response to methylglyoxal / glyoxalase III activity / thiolester hydrolase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / protein repair / guanine deglycation / protein deglycase / protein deglycase activity / RNA repair ...D-lactate dehydratase / response to methylglyoxal / glyoxalase III activity / thiolester hydrolase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / protein repair / guanine deglycation / protein deglycase / protein deglycase activity / RNA repair / Hydrolases; Acting on ester bonds; Thioester hydrolases / response to acidic pH / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / DNA repair / protein homodimerization activity / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Protein/nucleic acid deglycase HchA / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein/nucleic acid deglycase 1 / Protein/nucleic acid deglycase HchA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCha, S.S. / Lee, S.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structures of human DJ-1 and Escherichia coli Hsp31, which share an evolutionarily conserved domain
Authors: Lee, S.J. / Kim, S.J. / Kim, I.K. / Ko, J. / Jeong, C.S. / Kim, G.H. / Park, C. / Kang, S.O. / Suh, P.G. / Lee, H.S. / Cha, S.S.
History
DepositionOct 16, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 6, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp / entity_name_com ...chem_comp / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num ..._entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hsp31
B: Hsp31


Theoretical massNumber of molelcules
Total (without water)62,4332
Polymers62,4332
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.910, 52.910, 316.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Hsp31


Mass: 31216.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XB78, UniProt: P31658*PLUS

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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: 2.18 Å3/Da / Density % sol: 43.1 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 Mammonium sulfate1reservoir
20.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1.12714 Å
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 4, 2002
RadiationMonochromator: Double crystal (silicone) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 12181 / Num. obs: 12181 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.9 Å2
Reflection shellResolution: 2.8→2.9 Å / % possible all: 98.6
Reflection
*PLUS
Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.167

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.83 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 303320.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1258 10.3 %RANDOM
Rwork0.218 ---
obs0.218 12181 99.6 %-
all-12181 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.0443 Å2 / ksol: 0.395536 e/Å3
Displacement parametersBiso mean: 13.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å27.77 Å20 Å2
2--0.55 Å20 Å2
3----1.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4194 0 0 0 4194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 202 10.1 %
Rwork0.248 1795 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.422
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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