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- PDB-8xsg: Crystal structure of the Actinobacillus minor NM305 glucosyltrans... -

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Basic information

Entry
Database: PDB / ID: 8xsg
TitleCrystal structure of the Actinobacillus minor NM305 glucosyltransferase in complex with UDP
ComponentsPutative glycosyltransferase
KeywordsTRANSFERASE / glycosylation / glycosyltransferase / glucosyltransferase / GT-B fold / UDP
Function / homology: / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / URIDINE / Putative glycosyltransferase
Function and homology information
Biological speciesActinobacillus minor NM305 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYamasaki, T. / Kohda, D.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K14138 Japan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: An uncharacterized gene from the Actinobacillus genus encodes a glucosyltransferase with successive transfer activity and unique substrate specificity.
Authors: Yamasaki, T. / Kohda, D.
History
DepositionJan 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0593
Polymers39,6201
Non-polymers4392
Water3,873215
1
A: Putative glycosyltransferase
hetero molecules

A: Putative glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1196
Polymers79,2402
Non-polymers8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3750 Å2
ΔGint-13 kcal/mol
Surface area30970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.136, 43.390, 95.823
Angle α, β, γ (deg.)90.000, 117.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-590-

HOH

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Components

#1: Protein Putative glycosyltransferase


Mass: 39619.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GLY A 1 EXPRESSION TAG PRO A 2 EXPRESSION TAG / Source: (gene. exp.) Actinobacillus minor NM305 (bacteria) / Gene: AM305_00150 / Production host: Escherichia coli (E. coli) / References: UniProt: C5RYK2
#2: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.2 M sodium formate, 14% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 32975 / % possible obs: 96.7 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Net I/σ(I): 33
Reflection shellResolution: 1.8→1.84 Å / Num. unique obs: 1948 / CC1/2: 0.989

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8XSH

8xsh


Resolution: 1.8→42.557 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.161 / SU B: 5.731 / SU ML: 0.08 / Average fsc free: 0.9743 / Average fsc work: 0.9869 / Cross valid method: FREE R-VALUE / ESU R: 0.259 / ESU R Free: 0.116
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2013 1696 5.143 %
Rwork0.1584 31278 -
all0.161 --
obs-32974 96.339 %
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: 28.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.838 Å20 Å2-0.585 Å2
2---0.417 Å2-0 Å2
3---0.121 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2796 0 29 215 3040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122896
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162707
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.6543914
X-RAY DIFFRACTIONr_angle_other_deg0.5151.5736247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8045341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.498518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24810503
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.20710148
X-RAY DIFFRACTIONr_chiral_restr0.0740.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02690
X-RAY DIFFRACTIONr_nbd_refined0.2170.2522
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22447
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21412
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2174
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1860.212
X-RAY DIFFRACTIONr_nbd_other0.1420.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1060.217
X-RAY DIFFRACTIONr_mcbond_it2.0552.7931367
X-RAY DIFFRACTIONr_mcbond_other2.0462.7931367
X-RAY DIFFRACTIONr_mcangle_it2.8375.0221707
X-RAY DIFFRACTIONr_mcangle_other2.8425.0241708
X-RAY DIFFRACTIONr_scbond_it2.3173.1611529
X-RAY DIFFRACTIONr_scbond_other2.3153.1611527
X-RAY DIFFRACTIONr_scangle_it3.215.652207
X-RAY DIFFRACTIONr_scangle_other3.215.6492208
X-RAY DIFFRACTIONr_lrange_it4.1128.053234
X-RAY DIFFRACTIONr_lrange_other4.01927.9413200
X-RAY DIFFRACTIONr_rigid_bond_restr3.98135603
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
1.8-1.8470.2311120.18422940.18725040.9760.98696.08630.168
1.847-1.8970.2511080.17320900.17624440.960.98789.93450.154
1.897-1.9520.2121100.15521180.15824140.9730.98692.29490.135
1.952-2.0120.2131150.13621100.1422820.9720.98997.50220.123
2.012-2.0780.1981160.14220690.14522300.9740.98897.98210.128
2.078-2.1510.2041220.14520120.14821760.9750.98898.06990.133
2.151-2.2320.1981220.13919210.14320840.9790.98998.03260.13
2.232-2.3220.2031060.14418570.14820010.9730.98898.1010.136
2.322-2.4250.1851060.12918110.13219520.9790.99198.2070.124
2.425-2.5430.186990.14317350.14518650.9780.98998.33780.139
2.543-2.680.238790.15216400.15617520.9720.98798.11640.15
2.68-2.8420.227850.16715760.17116880.9670.98398.40050.167
2.842-3.0380.237720.17414590.17715720.9650.98297.39190.178
3.038-3.280.196600.17213420.17314610.9780.98395.96170.178
3.28-3.590.207560.1810950.18113690.9760.98584.0760.19
3.59-4.0110.186570.15911480.1612230.980.98798.52820.173
4.011-4.6240.195640.14210290.14510990.9830.98999.4540.163
4.624-5.6470.168330.1578910.1589260.9830.98999.7840.181
5.647-7.9170.208440.1717010.1747450.9740.9851000.189
7.917-42.5570.16300.2043800.2014370.9860.97893.82150.239

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