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- PDB-3d3i: Crystal structural of Escherichia coli K12 YgjK, a glucosidase be... -

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Basic information

Entry
Database: PDB / ID: 3d3i
TitleCrystal structural of Escherichia coli K12 YgjK, a glucosidase belonging to glycoside hydrolase family 63
ComponentsUncharacterized protein ygjK
KeywordsHYDROLASE / GH63 / processing alpha-glucosidase / alpha/alpha barrel
Function / homology
Function and homology information


glucosidase complex / alpha,alpha-trehalase activity / trehalose catabolic process / glucosidase activity / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / oligosaccharide catabolic process / DNA damage response / metal ion binding
Similarity search - Function
Ribosomal protein L30p/L7e / : / Glucosidase YgjK, N-terminal / putative glycoside hydrolase family protein from bacillus halodurans / Glycoside hydrolase, family 37 / Helix Hairpins - #100 / : / Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / Ribosomal Protein L30; Chain: A, / Glycosyltransferase - #10 ...Ribosomal protein L30p/L7e / : / Glucosidase YgjK, N-terminal / putative glycoside hydrolase family protein from bacillus halodurans / Glycoside hydrolase, family 37 / Helix Hairpins - #100 / : / Mannosylglycerate hydrolase MGH1-like glycoside hydrolase domain / Ribosomal Protein L30; Chain: A, / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsKurakata, Y. / Uechi, A. / Yoshida, H. / Kamitori, S. / Sakano, Y. / Nishikawa, A. / Tonozuka, T.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63.
Authors: Kurakata, Y. / Uechi, A. / Yoshida, H. / Kamitori, S. / Sakano, Y. / Nishikawa, A. / Tonozuka, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary X-ray analysis of Escherichia coli K12 YgjK protein, a member of glycosyl hydrolase family 63
Authors: Tonozuka, T. / Uechi, A. / Mizuno, M. / Ichikawa, K. / Nishikawa, A. / Sakano, Y.
History
DepositionMay 12, 2008Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 3, 2008ID: 2DS3
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Uncharacterized protein ygjK
B: Uncharacterized protein ygjK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,0078
Polymers173,5592
Non-polymers4496
Water36,1022004
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein ygjK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0044
Polymers86,7791
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Uncharacterized protein ygjK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0044
Polymers86,7791
Non-polymers2243
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.6870, 138.5490, 87.5430
Angle α, β, γ (deg.)90, 96.60, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein ygjK


Mass: 86779.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: ygjK, b3080, JW3051 / Plasmid: pYgjK-SIG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42592
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2004 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 20% PEG 8000, 0.6M magnesium chloride, 100mM Tris-HCl buffer, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 139299

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→50 Å
RfactorNum. reflection
Rfree0.201 -
Rwork0.169 -
obs-139134
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12106 0 26 2004 14136

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