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- PDB-7vkw: The apo structure of beta-1,2-glucosyltransferase from Ignavibact... -

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Basic information

Entry
Database: PDB / ID: 7vkw
TitleThe apo structure of beta-1,2-glucosyltransferase from Ignavibacterium album
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
Beta-1,2-glucosyltransferase
Similarity search - Component
Biological speciesIgnavibacterium album (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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


Theoretical massNumber of molelcules
Total (without water)169,6942
Polymers169,6942
Non-polymers00
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-4 kcal/mol
Surface area49990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.649, 71.680, 129.980
Angle α, β, γ (deg.)90.000, 105.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 84846.789 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris-HCl (pH 7.5), 0.2M calcium acetate, 20%(w/v) PEG 3350
PH range: 7.5

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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: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→65.33 Å / Num. obs: 146514 / % possible obs: 99.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 17.7
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 6 / Num. unique obs: 7086 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→65.329 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.98 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.107 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1973 7304 4.993 %
Rwork0.1619 138988 -
all0.164 --
obs-146292 99.376 %
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: 14.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.75→65.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11651 0 0 729 12380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01311951
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611256
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.6416137
X-RAY DIFFRACTIONr_angle_other_deg1.4531.58125969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97451405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45923.498646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.065152148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9351546
X-RAY DIFFRACTIONr_chiral_restr0.0890.21513
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022876
X-RAY DIFFRACTIONr_nbd_refined0.2110.22301
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.210833
X-RAY DIFFRACTIONr_nbtor_refined0.180.25875
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.25633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2659
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.170.214
X-RAY DIFFRACTIONr_nbd_other0.2010.274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.214
X-RAY DIFFRACTIONr_mcbond_it1.4031.3295632
X-RAY DIFFRACTIONr_mcbond_other1.4021.3295631
X-RAY DIFFRACTIONr_mcangle_it2.0941.9887033
X-RAY DIFFRACTIONr_mcangle_other2.0941.9887034
X-RAY DIFFRACTIONr_scbond_it2.2611.5776319
X-RAY DIFFRACTIONr_scbond_other2.261.5786320
X-RAY DIFFRACTIONr_scangle_it3.5292.2539104
X-RAY DIFFRACTIONr_scangle_other3.5292.2539105
X-RAY DIFFRACTIONr_lrange_it4.46115.63113702
X-RAY DIFFRACTIONr_lrange_other4.43715.52213553
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
1.75-1.7950.2344670.186100880.189108510.9270.93497.27210.157
1.795-1.8450.2084740.16998590.171105260.9390.94998.16650.142
1.845-1.8980.2125320.16795960.17102490.9390.9598.81940.142
1.898-1.9560.2064740.16793990.16999830.9420.95198.89810.147
1.956-2.020.2034720.16290840.16496490.9470.95599.03620.143
2.02-2.0910.1954540.15988870.16193860.950.95899.52060.144
2.091-2.170.1954940.16185350.16290360.9490.95899.92250.146
2.17-2.2590.2063980.15982820.16186820.9490.95899.9770.146
2.259-2.3590.2024400.15379280.15583680.9490.961000.139
2.359-2.4740.1974210.14875580.15179790.9520.9641000.138
2.474-2.6080.2133890.15671890.15975780.9450.9591000.148
2.608-2.7650.1733820.15768330.15772150.9580.9621000.149
2.765-2.9560.2243300.16764200.1767590.940.95699.86680.162
2.956-3.1920.2143110.17759700.17862810.9390.9511000.175
3.192-3.4960.1922890.17555300.17658260.9550.95999.87990.176
3.496-3.9080.2032710.16750230.16952960.9490.96199.96220.173
3.908-4.5090.1532290.13844290.13946760.9760.97799.61510.147
4.509-5.5160.172340.14837110.14939450.9750.981000.16
5.516-7.7730.2171530.17529450.17730980.960.9671000.183
7.773-65.3290.173880.17216790.17217800.9720.96899.26970.199

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