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- PDB-7vl4: The complex structure of beta-1,2-glucosyltransferase from Ignavi... -

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Basic information

Entry
Database: PDB / ID: 7vl4
TitleThe complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with methyl beta-D-glucoside
Componentsbeta-1,2-glucosyltransferase
KeywordsTRANSFERASE / beta-1 / 2-glucosyltransferase Glycoside / hydrolase family 35 / HYDROLASE
Function / homology
Function and homology information


beta-1,2-glucosyltransferase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding / cytoplasm
Similarity search - Function
: / GLMA-like, second domain / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
methyl beta-D-glucopyranoside / Beta-1,2-glucosyltransferase
Similarity search - Component
Biological speciesIgnavibacterium album (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsKobayashi, K. / Shimizu, H. / Tanaka, N. / Kuramochi, K. / Nakai, H. / Nakajima, M. / Taguchi, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K05830 Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Characterization and structural analyses of a novel glycosyltransferase acting on the beta-1,2-glucosidic linkages.
Authors: Kobayashi, K. / Shimizu, H. / Tanaka, N. / Kuramochi, K. / Nakai, H. / Nakajima, M. / Taguchi, H.
History
DepositionOct 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta-1,2-glucosyltransferase
B: beta-1,2-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7605
Polymers166,3322
Non-polymers4283
Water17,240957
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-4 kcal/mol
Surface area49340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.949, 71.650, 130.110
Angle α, β, γ (deg.)90.000, 105.590, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-1,2-glucosyltransferase / Beta-galactosidase


Mass: 83165.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ignavibacterium album (strain DSM 19864 / JCM 16511 / NBRC 101810 / Mat9-16) (bacteria)
Strain: DSM 19864 / JCM 16511 / NBRC 101810 / Mat9-16 / Gene: IALB_1185 / Plasmid: pET30a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: I0AIT9
#2: Sugar ChemComp-MGL / methyl beta-D-glucopyranoside / O1-METHYL-GLUCOSE / methyl beta-D-glucoside / methyl D-glucoside / methyl glucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcp[1Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-b-D-glucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-glucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 957 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl (pH 7.5), 0.2M calcium acetate, 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→47.99 Å / Num. obs: 126164 / % possible obs: 98.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.4
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6096 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→19.978 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.317 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2085 6227 4.989 %
Rwork0.1713 118589 -
all0.173 --
obs-124816 97.337 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.267 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å2-0 Å20.001 Å2
2--0.001 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.83→19.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11666 0 27 957 12650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312007
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611298
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.64316217
X-RAY DIFFRACTIONr_angle_other_deg1.3461.58426076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01451411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68823.509647
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.729152153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7891546
X-RAY DIFFRACTIONr_chiral_restr0.0770.21527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022881
X-RAY DIFFRACTIONr_nbd_refined0.2030.22401
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.210865
X-RAY DIFFRACTIONr_nbtor_refined0.1750.25857
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.25510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2886
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1820.22
X-RAY DIFFRACTIONr_metal_ion_refined0.050.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.216
X-RAY DIFFRACTIONr_nbd_other0.1650.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.239
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1280.21
X-RAY DIFFRACTIONr_mcbond_it1.3181.4425650
X-RAY DIFFRACTIONr_mcbond_other1.3181.4425649
X-RAY DIFFRACTIONr_mcangle_it2.0932.1557059
X-RAY DIFFRACTIONr_mcangle_other2.0932.1557060
X-RAY DIFFRACTIONr_scbond_it1.9651.6566357
X-RAY DIFFRACTIONr_scbond_other1.9651.6566357
X-RAY DIFFRACTIONr_scangle_it3.1722.3859158
X-RAY DIFFRACTIONr_scangle_other3.1722.3859159
X-RAY DIFFRACTIONr_lrange_it4.63117.04714003
X-RAY DIFFRACTIONr_lrange_other4.56216.86113792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.83-1.8770.3034350.27286160.27393880.7820.78996.41030.24
1.877-1.9280.2674480.24483390.24590920.850.85896.64540.209
1.928-1.9830.2494260.22681980.22789070.8760.87996.82270.192
1.983-2.0440.2514070.20679410.20886150.8850.90296.90080.171
2.044-2.110.234230.19577080.19783670.9140.9297.17940.165
2.11-2.1830.2073670.18274850.18480720.9270.93197.27450.154
2.183-2.2640.2223840.17672160.17877990.9220.93697.44840.147
2.264-2.3560.2163500.16470410.16775740.9290.94597.58380.138
2.356-2.4590.2053480.15367160.15572310.9390.95497.69050.129
2.459-2.5770.1983420.1564110.15269010.9450.95697.85540.128
2.577-2.7140.1893250.14861420.1566070.9530.9697.8810.129
2.714-2.8750.2053210.15458270.15662740.9420.95697.99170.136
2.875-3.0690.2022780.15855090.1659000.9460.95798.08470.145
3.069-3.3090.2072590.16951410.17155020.9440.95198.14610.159
3.309-3.6140.1812580.16147080.16250550.9610.96598.23940.157
3.614-4.0250.1782160.14443180.14546050.9670.97398.45820.143
4.025-4.6160.1642130.12838180.1341340.9720.97897.50850.132
4.616-5.580.1971790.15131720.15435190.9680.97395.22590.16
5.58-7.60.1991320.17726320.17827870.9650.96599.17470.179
7.6-19.9780.1841160.16616510.16717820.9690.97399.15820.184

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