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- PDB-4i46: Crystal structure of 31kD Heat Shock Protein, VcHsp31 from Vibrio... -

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Basic information

Entry
Database: PDB / ID: 4i46
TitleCrystal structure of 31kD Heat Shock Protein, VcHsp31 from Vibrio cholerae
ComponentsIntracellular protease/amidase
KeywordsHYDROLASE / alpha-beta domains / chaperone-protease
Function / homology
Function and homology information


D-lactate dehydratase / glyoxalase III activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / protein deglycase activity / DNA repair / cytoplasm
Similarity search - Function
Protein/nucleic acid deglycase HchA / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-lactate dehydratase / DJ-1_PfpI domain-containing protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSen, U. / Das, S.
CitationJournal: To be Published
Title: Temperature dependent structural flexibility and functional activation of 31kD Heat Shock Protein, VcHsp31 from Vibrio cholerae
Authors: Das, S. / Sen, U.
History
DepositionNov 27, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Intracellular protease/amidase
B: Intracellular protease/amidase
C: Intracellular protease/amidase
D: Intracellular protease/amidase
E: Intracellular protease/amidase
F: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,91412
Polymers188,2056
Non-polymers7096
Water12,466692
1
A: Intracellular protease/amidase
B: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0895
Polymers62,7352
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-44 kcal/mol
Surface area21520 Å2
MethodPISA
2
C: Intracellular protease/amidase
D: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8533
Polymers62,7352
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-18 kcal/mol
Surface area21680 Å2
MethodPISA
3
E: Intracellular protease/amidase
F: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9714
Polymers62,7352
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4862
Polymers31,3671
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: Intracellular protease/amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4862
Polymers31,3671
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.287, 80.030, 133.037
Angle α, β, γ (deg.)90.00, 95.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Intracellular protease/amidase


Mass: 31367.426 Da / Num. of mol.: 6 / Fragment: Heat Shock Protein 31
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Ogawa 395 / O395 / Gene: A5F0Q0, VC0395_0351, VC395_A0912 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A5F0Q0, UniProt: A0A0H3AFW5*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: 5% PEG6000, 10% MPD, pH 5.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 5, 2012
RadiationMonochromator: Cu K -alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 48750 / Num. obs: 94575 / % possible obs: 91.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 32.6 Å2
Reflection shellResolution: 2.5→30 Å / % possible all: 91

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Processing

Software
NameClassification
MAR345dtbdata collection
CNSrefinement
AUTOMARdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.65 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1891954.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2455 5 %RANDOM
Rwork0.199 ---
all0.199 ---
obs0.199 48750 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.9985 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å212.1 Å2
2---1.41 Å20 Å2
3---3.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12978 0 48 692 13718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_mcbond_it1.28
X-RAY DIFFRACTIONc_mcangle_it2.11
X-RAY DIFFRACTIONc_scbond_it1.9
X-RAY DIFFRACTIONc_scangle_it2.73
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.359 295 4.9 %
Rwork0.302 5717 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4MPD.paramMPD.top

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