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- PDB-7vl6: The complex structure of beta-1,2-glucosyltransferase from Ignavi... -

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Basic information

Entry
Database: PDB / ID: 7vl6
TitleThe complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with arbutin
Componentsbeta-1,2-glucosyltransferase
KeywordsTRANSFERASE / beta-1 / 2-glucosyltransferase Glycoside hydrolase family 35 / HYDROLASE
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
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
Chem-7OQ / Beta-galactosidase
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

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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)166,9165
Polymers166,3322
Non-polymers5853
Water17,925995
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-12 kcal/mol
Surface area49960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.530, 71.846, 130.716
Angle α, β, γ (deg.)90.000, 104.990, 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: Chemical ChemComp-7OQ / (2R,3S,4S,5R,6S)-2-(hydroxymethyl)-6-(4-oxidanylphenoxy)oxane-3,4,5-triol


Mass: 272.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16O7 / Feature type: SUBJECT OF INVESTIGATION
#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.: 995 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
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 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→48.09 Å / Num. obs: 149359 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7279 / % 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: 1.75→19.999 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.435 / SU ML: 0.076 / 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
Rfree0.1966 7448 4.99 %
Rwork0.161 141797 -
all0.163 --
obs-149245 99.914 %
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: 17.259 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11651 0 39 995 12685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312014
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611298
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.64516229
X-RAY DIFFRACTIONr_angle_other_deg1.3941.58426073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88451411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98223.498646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.977152152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.211546
X-RAY DIFFRACTIONr_chiral_restr0.0850.21527
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022889
X-RAY DIFFRACTIONr_nbd_refined0.2070.22242
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1730.210415
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25793
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.25345
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2817
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1680.215
X-RAY DIFFRACTIONr_nbd_other0.1750.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0590.21
X-RAY DIFFRACTIONr_mcbond_it1.51.6145647
X-RAY DIFFRACTIONr_mcbond_other1.4971.6145646
X-RAY DIFFRACTIONr_mcangle_it2.22.4137057
X-RAY DIFFRACTIONr_mcangle_other2.1992.4137058
X-RAY DIFFRACTIONr_scbond_it2.3641.8746367
X-RAY DIFFRACTIONr_scbond_other2.3641.8746368
X-RAY DIFFRACTIONr_scangle_it3.7132.6939172
X-RAY DIFFRACTIONr_scangle_other3.7132.6939173
X-RAY DIFFRACTIONr_lrange_it4.79919.10413744
X-RAY DIFFRACTIONr_lrange_other4.79919.10513745
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
1.75-1.7950.2994890.252104400.254109290.8520.8571000.226
1.795-1.8440.2544840.23101940.231106780.8780.8891000.2
1.844-1.8970.2445330.20697210.208102540.90.9091000.175
1.897-1.9550.2354900.18895710.19100620.910.92799.99010.156
1.955-2.0180.2164750.17793030.17997780.9280.9371000.15
2.018-2.0880.1964780.16589820.16694600.9450.951000.141
2.088-2.1660.2024720.16186090.16390810.9430.9531000.139
2.166-2.2540.1964300.15784240.15988540.9480.9551000.136
2.254-2.3520.1924170.1579230.15283400.950.961000.128
2.352-2.4650.1964290.14276880.14581170.9510.9631000.123
2.465-2.5970.1924060.14172600.14476670.9510.96499.9870.124
2.597-2.7510.1883810.1569160.15272980.9540.96199.98630.132
2.751-2.9370.2013250.15465290.15668550.950.96199.98540.138
2.937-3.1670.1993330.16260670.16464010.9490.95999.98440.149
3.167-3.460.2012930.16556390.16759330.9540.96299.98310.157
3.46-3.8550.192750.15550830.15753590.9590.96799.98130.151
3.855-4.4240.1562360.12845580.12947940.9750.9781000.128
4.424-5.3530.1472340.13538680.13641020.9790.9821000.136
5.353-7.3120.1911690.15830780.15932470.9670.9711000.155
7.312-19.9990.173990.1619440.16120430.9750.9721000.163

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