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- PDB-7vl5: The complex structure of beta-1,2-glucosyltransferase from Ignavi... -

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Basic information

Entry
Database: PDB / ID: 7vl5
TitleThe complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with n-octyl-beta-D-glucoside
ComponentsBeta-galactosidase
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: 1.93 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-galactosidase
B: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,9575
Polymers166,3322
Non-polymers6253
Water13,691760
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-2 kcal/mol
Surface area48700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.142, 71.590, 129.914
Angle α, β, γ (deg.)90.000, 106.024, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 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-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC 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.: 760 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
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: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→47.89 Å / Num. obs: 108358 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.8
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5326 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→19.986 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.046 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.162 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2125 5443 5.028 %
Rwork0.17 102804 -
all0.172 --
obs-108247 99.881 %
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: 21.528 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0.004 Å2-0 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 1.93→19.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11651 0 41 760 12452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01311991
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611303
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.64416187
X-RAY DIFFRACTIONr_angle_other_deg1.3321.58826089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35551405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01823.498646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.961152148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5051546
X-RAY DIFFRACTIONr_chiral_restr0.0750.21523
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022875
X-RAY DIFFRACTIONr_nbd_refined0.1990.22470
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.211109
X-RAY DIFFRACTIONr_nbtor_refined0.1750.25882
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.25582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2824
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1010.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.218
X-RAY DIFFRACTIONr_nbd_other0.1820.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.229
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1290.21
X-RAY DIFFRACTIONr_mcbond_it1.6522.0895632
X-RAY DIFFRACTIONr_mcbond_other1.6522.0885631
X-RAY DIFFRACTIONr_mcangle_it2.4663.1257033
X-RAY DIFFRACTIONr_mcangle_other2.4653.1257034
X-RAY DIFFRACTIONr_scbond_it2.382.3436359
X-RAY DIFFRACTIONr_scbond_other2.382.3436359
X-RAY DIFFRACTIONr_scangle_it3.7963.3969154
X-RAY DIFFRACTIONr_scangle_other3.7963.3969155
X-RAY DIFFRACTIONr_lrange_it4.94324.32914009
X-RAY DIFFRACTIONr_lrange_other4.91124.20913851
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
1.93-1.980.2994070.24975170.25179240.820.8391000.22
1.98-2.0330.2843690.23673210.23876910.8510.86699.9870.203
2.033-2.0920.2613930.2170760.21374700.8770.89799.98660.18
2.092-2.1550.2663420.20769390.20972820.8850.90599.98630.174
2.155-2.2250.2443750.1967050.19370810.9060.92199.98590.157
2.225-2.3020.2453210.18264990.18568200.9130.9261000.151
2.302-2.3880.2253330.17862670.1866010.9240.93299.98480.147
2.388-2.4840.2112950.1660900.16263850.9380.9481000.13
2.484-2.5930.2123080.15758050.1661130.9410.9521000.128
2.593-2.7170.2212980.16655530.16958510.9380.9481000.138
2.717-2.8610.223000.15652910.1655910.9360.9531000.132
2.861-3.0310.2142790.17149570.17452370.9410.9599.98090.148
3.031-3.2340.2242570.17447210.17749790.9380.95199.97990.156
3.234-3.4860.2022290.17744170.17846470.9530.95899.97850.164
3.486-3.8070.1952020.16341080.16543120.960.96699.95360.151
3.807-4.2370.1661940.13137250.13339190.970.9761000.122
4.237-4.8570.1551850.12332780.12534630.9760.9811000.116
4.857-5.8620.1751590.14628360.14829950.9740.9791000.137
5.862-7.9550.1941220.1622520.16223740.9580.971000.148
7.955-19.9860.152750.16714470.16615220.9810.981000.165

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