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- PDB-7x87: The complex structure of beta-1,2-glucosyltransferase from Ignavi... -

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Basic information

Entry
Database: PDB / ID: 7x87
TitleThe complex structure of beta-1,2-glucosyltransferase from Ignavibacterium album with sophotetraose observed as sophorose
ComponentsBeta-galactosidase
KeywordsTRANSFERASE / beta-1 / 2-glucosyltransferase / Glycoside hydrolase family 35
Function / homologyGlycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Class I glutamine amidotransferase-like / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / carbohydrate metabolic process / metal ion binding / Beta-galactosidase
Function and homology information
Biological speciesIgnavibacterium album (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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
DepositionMar 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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)170,1947
Polymers169,6922
Non-polymers5035
Water15,547863
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-26 kcal/mol
Surface area50010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.135, 71.615, 130.308
Angle α, β, γ (deg.)90.000, 104.894, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-galactosidase


Mass: 84845.805 Da / Num. of mol.: 2 / Mutation: E343Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ignavibacterium album (bacteria) / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I0AIT9
#2: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 863 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
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) PEG3350

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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: Apr 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→47.93 Å / Num. obs: 138455 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.995 / Net I/σ(I): 9.4
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6743 / CC1/2: 0.57 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VKW

7vkw


Resolution: 1.79→47.905 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.154 / SU B: 2.725 / SU ML: 0.082 / Average fsc free: 0.9289 / Average fsc work: 0.9375 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2005 6808 4.917 %
Rwork0.1663 131642 -
all0.168 --
obs-138450 99.969 %
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: 17.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.02 Å2
2---0.011 Å20 Å2
3----0.008 Å2
Refinement stepCycle: LAST / Resolution: 1.79→47.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11687 0 27 863 12577
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01312019
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611307
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.64316233
X-RAY DIFFRACTIONr_angle_other_deg1.3811.58326094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00451411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08223.513649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.266152156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7661546
X-RAY DIFFRACTIONr_chiral_restr0.0830.21528
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213485
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022887
X-RAY DIFFRACTIONr_nbd_refined0.2080.22261
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.210761
X-RAY DIFFRACTIONr_nbtor_refined0.1770.25812
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.25428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2783
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0490.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1490.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.350.218
X-RAY DIFFRACTIONr_nbd_other0.30.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1190.218
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0870.21
X-RAY DIFFRACTIONr_mcbond_it1.5181.6635653
X-RAY DIFFRACTIONr_mcbond_other1.5051.6635652
X-RAY DIFFRACTIONr_mcangle_it2.2552.4867061
X-RAY DIFFRACTIONr_mcangle_other2.2552.4867062
X-RAY DIFFRACTIONr_scbond_it2.2831.9136366
X-RAY DIFFRACTIONr_scbond_other2.2831.9136367
X-RAY DIFFRACTIONr_scangle_it3.6252.7559172
X-RAY DIFFRACTIONr_scangle_other3.6252.7559173
X-RAY DIFFRACTIONr_lrange_it4.82219.38113756
X-RAY DIFFRACTIONr_lrange_other4.82219.38113757
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
1.79-1.8360.3154760.2797140.272102160.8230.83399.74550.263
1.836-1.8870.2815010.23793680.23998700.8610.87899.98990.225
1.887-1.9410.2364740.21291780.21396520.9030.911000.196
1.941-2.0010.2264630.19389080.19493710.9170.9251000.176
2.001-2.0660.2194660.18486060.18590720.9260.9341000.165
2.066-2.1390.2084090.17384160.17488250.9340.9431000.156
2.139-2.2190.1924470.16180560.16385030.9470.9521000.144
2.219-2.310.1983940.15577910.15781850.9470.9571000.138
2.31-2.4120.2043790.15574600.15878390.9450.9541000.137
2.412-2.530.1873790.14671030.14874820.9530.9611000.13
2.53-2.6660.1923180.14968640.15171830.9510.96399.98610.134
2.666-2.8270.1893130.15164360.15367490.9530.9621000.136
2.827-3.0220.1992960.16160900.16363860.950.9591000.149
3.022-3.2630.1993150.17156420.17359570.9510.9581000.164
3.263-3.5730.1982810.17251900.17354730.950.96299.96350.168
3.573-3.9910.172790.14746740.14949540.9680.97399.97980.148
3.991-4.6040.1592120.12741620.12943740.9750.9811000.131
4.604-5.6250.1761850.14835900.14937750.9790.9821000.153
5.625-7.9010.1911420.16627720.16829140.9660.9711000.169
7.901-47.9050.197790.15716230.15917040.9630.97499.88260.179

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