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- PDB-9we5: UDP-Glucose-bound UgtP with deletion of Pro48-Met91 and insertion... -

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Basic information

Entry
Database: PDB / ID: 9we5
TitleUDP-Glucose-bound UgtP with deletion of Pro48-Met91 and insertion of a Ser-Ser-Ser linker
ComponentsProcessive diacylglycerol beta-glucosyltransferase
KeywordsTRANSFERASE / Processive diacylglycerol beta-glucosyltransferase
Function / homology
Function and homology information


diglucosyl diacylglycerol synthase (1,6-linking) / 1,2-diacylglycerol 3-glucosyltransferase activity / enterobacterial common antigen biosynthetic process / lipoteichoic acid biosynthetic process / glycolipid biosynthetic process / plasma membrane
Similarity search - Function
Processive diacylglycerol beta-glucosyltransferase / Diacylglycerol glucosyltransferase, N-terminal / : / Monogalactosyldiacylglycerol (MGDG) synthase / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
Chem-660 / Processive diacylglycerol beta-glucosyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsFujishiro, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Structure of dimer form of UgtP
Authors: Fujishiro, T. / Matsuoka, S.
History
DepositionAug 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Processive diacylglycerol beta-glucosyltransferase
B: Processive diacylglycerol beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0564
Polymers78,9272
Non-polymers1,1292
Water00
1
A: Processive diacylglycerol beta-glucosyltransferase
hetero molecules

A: Processive diacylglycerol beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0564
Polymers78,9272
Non-polymers1,1292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6350 Å2
ΔGint-49 kcal/mol
Surface area30120 Å2
MethodPISA
2
B: Processive diacylglycerol beta-glucosyltransferase
hetero molecules

B: Processive diacylglycerol beta-glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0564
Polymers78,9272
Non-polymers1,1292
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area6540 Å2
ΔGint-52 kcal/mol
Surface area30660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.120, 64.080, 110.660
Angle α, β, γ (deg.)90.000, 107.234, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Processive diacylglycerol beta-glucosyltransferase / Beta-diglucosyldiacylglycerol synthase / Beta-DGS / DGlcDAG synthase / Glc2-DAG synthase / Beta- ...Beta-diglucosyldiacylglycerol synthase / Beta-DGS / DGlcDAG synthase / Glc2-DAG synthase / Beta-gentiobiosyldiacylglycerol synthase / Beta-monoglucosyldiacylglycerol synthase / Beta-MGS / MGlcDAG synthase / Beta-triglucosyldiacylglycerol synthase / TGlcDAG synthase / Diglucosyl diacylglycerol synthase (1 / 6-linking) / Glucosyl-beta-1 / 6-glucosyldiacylglycerol synthase / UDP glucosyltransferase / UDP-glucose:1 / 2-diacylglycerol-3-beta-D-glucosyltransferase


Mass: 39463.453 Da / Num. of mol.: 2
Mutation: deletion of Pro48-Met91,insertion of a Ser-Ser-Ser linker
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ugtP, ypfP, BSU21920 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: P54166, diglucosyl diacylglycerol synthase (1,6-linking)
#2: Chemical ChemComp-660 / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid / UDP-glucose phosphonate


Mass: 564.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N2O16P2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, 5% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.018 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 22, 2024
RadiationMonochromator: Cryo-cooled channel-cut Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.018 Å / Relative weight: 1
ReflectionResolution: 3.7→50 Å / Num. obs: 9535 / % possible obs: 99.4 % / Redundancy: 3.6 % / CC1/2: 0.989 / Rrim(I) all: 0.245 / Net I/σ(I): 5.49
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 1357 / CC1/2: 0.612 / Rrim(I) all: 1.153 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→48.045 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.949 / SU B: 160.8 / SU ML: 0.946 / Cross valid method: FREE R-VALUE / ESU R Free: 0.887
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3105 477 5.003 %
Rwork0.23 9058 -
all0.234 --
obs-9535 99.52 %
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: 129.425 Å2
Baniso -1Baniso -2Baniso -3
1--0.653 Å20 Å2-0.21 Å2
2---0.986 Å20 Å2
3---1.483 Å2
Refinement stepCycle: LAST / Resolution: 3.7→48.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5129 0 72 0 5201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125287
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1120.015097
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.6427162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7385642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26223.622254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.16515988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.221526
X-RAY DIFFRACTIONr_chiral_restr0.1320.2723
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023842
X-RAY DIFFRACTIONr_nbd_refined0.2710.22429
X-RAY DIFFRACTIONr_nbtor_refined0.3270.23473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2142
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2760.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0720.22
X-RAY DIFFRACTIONr_mcbond_it7.92311.2752586
X-RAY DIFFRACTIONr_mcangle_it13.33516.8883222
X-RAY DIFFRACTIONr_scbond_it8.1412.0322701
X-RAY DIFFRACTIONr_scangle_it13.82317.8733940
X-RAY DIFFRACTIONr_lrange_it25.224215.01621526
X-RAY DIFFRACTIONr_ncsr_local_group_10.1890.059216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.7960.356350.414659X-RAY DIFFRACTION99.8561
3.796-3.8990.435320.418622X-RAY DIFFRACTION98.051
3.899-4.0110.45330.398632X-RAY DIFFRACTION97.7941
4.011-4.1340.403320.28603X-RAY DIFFRACTION100
4.134-4.2690.315330.244614X-RAY DIFFRACTION100
4.269-4.4170.309280.233540X-RAY DIFFRACTION100
4.417-4.5830.448300.206576X-RAY DIFFRACTION100
4.583-4.7680.326280.205519X-RAY DIFFRACTION99.8175
4.768-4.9780.339270.193513X-RAY DIFFRACTION99.8152
4.978-5.2180.36260.179501X-RAY DIFFRACTION99.8106
5.218-5.4970.325240.174456X-RAY DIFFRACTION100
5.497-5.8260.376240.175457X-RAY DIFFRACTION99.7925
5.826-6.2230.281210.181406X-RAY DIFFRACTION100
6.223-6.7130.243210.197396X-RAY DIFFRACTION99.5227
6.713-7.340.307190.173366X-RAY DIFFRACTION100
7.34-8.1840.292180.186328X-RAY DIFFRACTION100
8.184-9.4090.27150.177290X-RAY DIFFRACTION100
9.409-11.4230.194130.166255X-RAY DIFFRACTION100
11.423-15.7480.227110.178200X-RAY DIFFRACTION99.061
15.748-48.0450.24170.426125X-RAY DIFFRACTION97.7778
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.72050.6285-0.46890.4386-0.20810.1343-0.0043-0.2181-0.0577-0.1332-0.0141-0.03120.02660.05110.01830.1350.0434-0.02010.1765-0.03740.0158-9.14711.59866.6731
21.1621-0.60840.22080.4047-0.17740.20930.09990.12620.1260.0228-0.0559-0.00970.00240.0808-0.0440.1462-0.00860.08590.1286-0.02260.074-25.63925.109346.0405
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 20
2X-RAY DIFFRACTION1ALLA21 - 142
3X-RAY DIFFRACTION1ALLA143 - 208
4X-RAY DIFFRACTION1ALLA209 - 261
5X-RAY DIFFRACTION1ALLA262 - 378
6X-RAY DIFFRACTION2ALLB1 - 132
7X-RAY DIFFRACTION2ALLB133 - 196
8X-RAY DIFFRACTION2ALLB197 - 273
9X-RAY DIFFRACTION2ALLB274 - 378

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