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- PDB-1ons: Crystal structure of Escherichia coli heat shock protein YedU -

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Basic information

Entry
Database: PDB / ID: 1ons
TitleCrystal structure of Escherichia coli heat shock protein YedU
ComponentsChaperone protein hchA
KeywordsCHAPERONE / heat shock protein / stress response / YedU / HSP31 / protease
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsZhao, Y. / Fox, R.O.
CitationJournal: Protein Sci. / Year: 2003
Title: The crystal structure of Escherichia coli heat shock protein YedU reveals three potential catalytic active sites
Authors: Zhao, Y. / Liu, D. / Kaluarachchi, W.D. / Bellamy, H.D. / White, M.A. / Fox, R.O.
History
DepositionFeb 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein hchA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1612
Polymers31,0951
Non-polymers651
Water2,162120
1
A: Chaperone protein hchA
hetero molecules

A: Chaperone protein hchA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3214
Polymers62,1902
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2080 Å2
ΔGint-51 kcal/mol
Surface area21630 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.98, 52.98, 347.40
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

21A-373-

HOH

31A-392-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: x, x-y+1, -z+1/6.

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Components

#1: Protein Chaperone protein hchA / Hsp31


Mass: 31095.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HCHA OR B1967 / Plasmid: PET30-XA-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P31658
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.2 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 600 and ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115.0 mg/mlprotein1drop
25 mMdithiothreitol1drop
310 mM1dropNaCl
420 mMTris1droppH8.2
52 %PEG6001reservoir
65 mMdithiothreitol1reservoir
71.8 Mammonium sulfate1reservoir
80.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 1.54 Å
DetectorType: MACSCIENCE / Detector: CCD / Date: Nov 12, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→90 Å / Num. all: 16033 / Num. obs: 15151 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.7
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.9 / % possible all: 77.5
Reflection
*PLUS
Num. measured all: 290299
Reflection shell
*PLUS
% possible obs: 77.5 % / Num. unique obs: 779 / Rmerge(I) obs: 0.319

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
XFITdata reduction
CNSrefinement
RefinementMethod to determine structure: MIR / Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 714 -RANDOM
Rwork0.204 ---
all0.22 15868 --
obs0.22 14856 93.6 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 1 120 2287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.006
LS refinement shellResolution: 2.2→2.25 Å
RfactorNum. reflection
Rfree0.2751 40
Rwork0.2404 -
obs-750
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.2 Å

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