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- PDB-5jzo: Structure of wild type amidase at high temperature at 2.5 Angstro... -

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Basic information

Entry
Database: PDB / ID: 5jzo
TitleStructure of wild type amidase at high temperature at 2.5 Angstrom resolution
ComponentsIntracellular protease/amidase
KeywordsLYASE / Heat Shock Protein
Function / homology
Function and homology information


D-lactate dehydratase / protein deglycase activity / DNA repair
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
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChowdhury, S.R. / Sen, U.
CitationJournal: To Be Published
Title: Structure of wild type amidase at high temperature at 2.5 Angstrom resolution
Authors: Chowdhury, S.R. / Sen, U.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)189,0696
Polymers189,0696
Non-polymers00
Water7,296405
1
A: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Intracellular protease/amidase


Theoretical massNumber of molelcules
Total (without water)31,5121
Polymers31,5121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.375, 80.069, 133.133
Angle α, β, γ (deg.)90.00, 95.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Intracellular protease/amidase / Uncharacterized protein


Mass: 31511.557 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_0351, VC395_A0912 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3AFW5, D-lactate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 5% PEG 6000, 0.1M sodium citrate, 8% MPD against a reservoir solution of 15% PEG 6000, 0.1M tris-HCl, pH-8.5, 5% MPD.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→29.668 Å / Num. obs: 49277 / % possible obs: 92.32 % / Redundancy: 1.94 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 1.39
Reflection shellResolution: 2.5→2.67 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N57

1n57


Resolution: 2.5→29.668 Å / SU ML: 0.38 / Cross valid method: NONE / σ(F): 1.39 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1999 4.06 %
Rwork0.1766 --
obs0.1798 49277 92.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→29.668 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12984 0 0 405 13389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813356
X-RAY DIFFRACTIONf_angle_d1.31518150
X-RAY DIFFRACTIONf_dihedral_angle_d15.3624782
X-RAY DIFFRACTIONf_chiral_restr0.0821902
X-RAY DIFFRACTIONf_plane_restr0.0092400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.33091450.25643420X-RAY DIFFRACTION94
2.5625-2.63170.36281430.23443403X-RAY DIFFRACTION94
2.6317-2.70910.30181440.22463418X-RAY DIFFRACTION94
2.7091-2.79650.30721450.21983425X-RAY DIFFRACTION95
2.7965-2.89640.31881460.21463426X-RAY DIFFRACTION94
2.8964-3.01220.33131450.21773440X-RAY DIFFRACTION94
3.0122-3.14920.30491450.20073435X-RAY DIFFRACTION94
3.1492-3.3150.30091450.1853432X-RAY DIFFRACTION94
3.315-3.52240.27031440.183413X-RAY DIFFRACTION94
3.5224-3.79380.21671440.15713392X-RAY DIFFRACTION93
3.7938-4.17470.19031420.13743357X-RAY DIFFRACTION91
4.1747-4.77660.2091400.13843319X-RAY DIFFRACTION91
4.7766-6.00980.25811400.16723285X-RAY DIFFRACTION89
6.0098-29.66970.21051310.16683113X-RAY DIFFRACTION83

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