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- PDB-4i4n: Crystal Structure of the catalytic Cys to Ala mutant of VcHsp31 f... -

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Basic information

Entry
Database: PDB / ID: 4i4n
TitleCrystal Structure of the catalytic Cys to Ala mutant of VcHsp31 from Vibrio cholerae
ComponentsIntracellular protease/amidase
KeywordsHYDROLASE / Dimer / alpha/beta hydrolase / Heat shock protein / chaperone / Amidopeptidase
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: 1.84 Å
AuthorsSen, U. / Das, S.
CitationJournal: To be Published
Title: Structural and Functional studies on Hsp31 of Vibrio cholere: Identification of a novel glutamate that attenuates the peptidase activity
Authors: Sen, U. / Das, S.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)183,8556
Polymers183,8556
Non-polymers00
Water9,656536
1
A: Intracellular protease/amidase
B: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)61,2852
Polymers61,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-5 kcal/mol
Surface area21290 Å2
MethodPISA
2
C: Intracellular protease/amidase
D: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)61,2852
Polymers61,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-5 kcal/mol
Surface area21370 Å2
MethodPISA
3
E: Intracellular protease/amidase
F: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)61,2852
Polymers61,2852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)30,6421
Polymers30,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
F: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)30,6421
Polymers30,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.750, 79.350, 107.650
Angle α, β, γ (deg.)90.00, 108.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Intracellular protease/amidase


Mass: 30642.451 Da / Num. of mol.: 6 / Mutation: C188A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Ogawa 395 / O395 / Gene: VC0395_0351, VC395_A0912 / Production host: Escherichia coli (E. coli) / References: UniProt: A5F0Q0, UniProt: A0A0H3AFW5*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8K, MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Nov 20, 2011
RadiationMonochromator: Nickel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.84→30 Å / Num. all: 143534 / Num. obs: 130793 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.9 Å2
Reflection shellResolution: 1.84→30 Å / % possible all: 91

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
AMoREphasing
CNS1.2refinement
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→29.36 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2266474.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.266 6528 5 %RANDOM
Rwork0.243 ---
all0.243 143534 --
obs0.243 130793 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.4379 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1-7.62 Å20 Å20.47 Å2
2---5.51 Å20 Å2
3----2.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.84→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12978 0 0 536 13514
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it32.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.84→1.92 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.383 761 4.8 %
Rwork0.342 15081 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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