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- PDB-1pv2: Native Form 2 E.coli Chaperone Hsp31 -

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Basic information

Entry
Database: PDB / ID: 1pv2
TitleNative Form 2 E.coli Chaperone Hsp31
ComponentsChaperone protein hchA
KeywordsCHAPERONE / Heat Shock Protein / Putative Catalytic Triad / Flexibility / monoclinic
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 / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsQuigley, P.M. / Korotkov, K. / Baneyx, F. / Hol, W.G.J.
CitationJournal: Protein Sci. / Year: 2004
Title: A new native EcHsp31 structure suggests a key role of structural flexibility for chaperone function.
Authors: Quigley, P.M. / Korotkov, K. / Baneyx, F. / Hol, W.G.J.
History
DepositionJun 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chaperone protein hchA
B: Chaperone protein hchA
C: Chaperone protein hchA
D: Chaperone protein hchA
E: Chaperone protein hchA
F: Chaperone protein hchA
G: Chaperone protein hchA
H: Chaperone protein hchA


Theoretical massNumber of molelcules
Total (without water)249,8118
Polymers249,8118
Non-polymers00
Water1,29772
1
A: Chaperone protein hchA
B: Chaperone protein hchA


Theoretical massNumber of molelcules
Total (without water)62,4532
Polymers62,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-7 kcal/mol
Surface area20050 Å2
MethodPISA
2
C: Chaperone protein hchA
D: Chaperone protein hchA


Theoretical massNumber of molelcules
Total (without water)62,4532
Polymers62,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-8 kcal/mol
Surface area20370 Å2
MethodPISA
3
E: Chaperone protein hchA
F: Chaperone protein hchA


Theoretical massNumber of molelcules
Total (without water)62,4532
Polymers62,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-8 kcal/mol
Surface area21070 Å2
MethodPISA
4
G: Chaperone protein hchA
H: Chaperone protein hchA


Theoretical massNumber of molelcules
Total (without water)62,4532
Polymers62,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-6 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.487, 99.018, 116.795
Angle α, β, γ (deg.)102.95, 101.52, 94.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Chaperone protein hchA / Hsp31


Mass: 31226.416 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: HCHA OR B1967 / Production host: Escherichia coli (E. coli) / References: UniProt: P31658
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 26% PEG 6000,50mM NaCl,100 mM Tris pH 7.5.5G, VAPOR DIFFUSION, SITTING DROP, temperature 22K, temperature 295K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
3100 mM1dropNaCl
41 mMEDTA1drop
54 mMdithiothreitol1drop
626 %PEG60001reservoir
750 mM1reservoirNaCl
8100 mMTris1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.77 Å
DetectorDetector: CCD / Date: Jan 13, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.71→48.8 Å / Num. all: 57067 / Num. obs: 57067 / % possible obs: 100 % / Observed criterion σ(I): 28 / Redundancy: 1.9 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2 / Num. unique all: 5883 / Rsym value: 0.339 / % possible all: 94.5
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 60105 / % possible obs: 96.1 %
Reflection shell
*PLUS
% possible obs: 94.1 % / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1n57

1n57


Resolution: 2.71→48.8 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.863 / SU B: 16.066 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.421
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.28635 3037 5.1 %RANDOM
Rwork0.22141 ---
all0.225 60105 --
obs0.22469 57067 94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.455 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20.1 Å2
2---0.17 Å20.19 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.71→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16161 0 0 72 16233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02116599
X-RAY DIFFRACTIONr_angle_refined_deg0.7611.95122508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.83252054
X-RAY DIFFRACTIONr_chiral_restr0.0570.22409
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212774
X-RAY DIFFRACTIONr_nbd_refined0.2310.38010
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.5880
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.375
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.512
X-RAY DIFFRACTIONr_mcbond_it2.3963.510348
X-RAY DIFFRACTIONr_mcangle_it4.536616518
X-RAY DIFFRACTIONr_scbond_it6.6518.8016251
X-RAY DIFFRACTIONr_scangle_it10.27312.55990
LS refinement shellResolution: 2.707→2.777 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.393 210
Rwork0.3 3732
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.004
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.793

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