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- PDB-7vl2: The complex structure of beta-1,2-glucosyltransferase from Ignavi... -

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Basic information

Entry
Database: PDB / ID: 7vl2
TitleThe complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with ethyl alpha-D-Glucoside
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-BW3 / Beta-galactosidase
Similarity search - Component
Biological speciesIgnavibacterium album (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 2.0Apr 6, 2022Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Revision 2.1May 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)166,5804
Polymers166,3322
Non-polymers2482
Water13,854769
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-7 kcal/mol
Surface area49470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.753, 71.517, 129.940
Angle α, β, γ (deg.)90.000, 105.131, 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-BW3 / (2~{S},3~{R},4~{S},5~{S},6~{R})-2-ethoxy-6-(hydroxymethyl)oxane-3,4,5-triol / Ethyl alpha-D-glucopyranoside


Type: D-saccharide, alpha linking / Mass: 208.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O6 / 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.: 769 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
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
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.84 Å / Num. obs: 135219 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2 / Num. unique obs: 6738 / % 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: 1.8→43.978 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.946 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2036 6793 5.024 %
Rwork0.1717 128424 -
all0.173 --
obs-135217 99.992 %
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: 18.185 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å2-0 Å2-0.001 Å2
2--0 Å20 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11642 0 15 769 12426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01311956
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611262
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.64216144
X-RAY DIFFRACTIONr_angle_other_deg1.3891.58325984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00851404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37623.488645
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.416152146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7051546
X-RAY DIFFRACTIONr_chiral_restr0.080.21517
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022874
X-RAY DIFFRACTIONr_nbd_refined0.2070.22343
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.210827
X-RAY DIFFRACTIONr_nbtor_refined0.1780.25852
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.25330
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2756
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.216
X-RAY DIFFRACTIONr_nbd_other0.2040.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1680.218
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1330.21
X-RAY DIFFRACTIONr_mcbond_it1.5191.7315628
X-RAY DIFFRACTIONr_mcbond_other1.5181.735627
X-RAY DIFFRACTIONr_mcangle_it2.2892.5887028
X-RAY DIFFRACTIONr_mcangle_other2.2892.5897029
X-RAY DIFFRACTIONr_scbond_it2.3071.9836328
X-RAY DIFFRACTIONr_scbond_other2.3071.9836329
X-RAY DIFFRACTIONr_scangle_it3.6412.8599116
X-RAY DIFFRACTIONr_scangle_other3.6412.8599117
X-RAY DIFFRACTIONr_lrange_it4.62920.16913783
X-RAY DIFFRACTIONr_lrange_other4.62920.1713784
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
1.8-1.8470.3025130.25894310.26199450.8280.83999.98990.231
1.847-1.8970.2644730.24192060.24296790.870.8721000.21
1.897-1.9520.2714470.21790220.2294690.8740.8921000.186
1.952-2.0120.2374970.20186230.20391200.9070.9151000.169
2.012-2.0780.214110.18584710.18688820.9290.9331000.155
2.078-2.1510.2364460.18481400.18785860.9190.9331000.156
2.151-2.2320.2164070.1778720.17282790.9330.9421000.144
2.232-2.3220.2144370.16475690.16780060.9360.951000.138
2.322-2.4250.1863870.15772760.15976630.9490.9531000.132
2.425-2.5430.1983660.15569410.15773070.9470.9571000.132
2.543-2.6810.1973770.1665830.16269600.9460.9561000.137
2.681-2.8420.2353320.16562980.16866300.9290.9521000.145
2.842-3.0380.1882820.16659050.16761870.9540.9571000.148
3.038-3.280.1922900.17355220.17358120.9550.9621000.16
3.28-3.5910.1962370.17751430.17853800.960.9621000.168
3.591-4.0120.1722690.15145470.15248160.970.9731000.146
4.012-4.6260.1522190.12640920.12743110.9760.981000.124
4.626-5.650.1641690.15134800.15136490.9750.9781000.148
5.65-7.9250.2021520.1727130.17128650.9620.9711000.163
7.925-43.9780.181820.18715900.18716720.9760.9751000.192

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