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- PDB-8jjt: Structure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms re... -

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Basic information

Entry
Database: PDB / ID: 8jjt
TitleStructure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms resolution
ComponentsTIGR04348 family glycosyltransferase
KeywordsTRANSFERASE / UDP-GlcNAc
Function / homologyPutative glycosyltransferase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / TIGR04348 family glycosyltransferase
Function and homology information
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsWei, H. / Feng, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To be published
Title: Structure of SenB in complex with UDP-GlcNAc at 1.88 Angstroms resolution
Authors: Wei, H. / Feng, L.
History
DepositionMay 31, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: TIGR04348 family glycosyltransferase
A: TIGR04348 family glycosyltransferase
B: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7986
Polymers105,9763
Non-polymers1,8223
Water14,592810
1
C: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9332
Polymers35,3251
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-5 kcal/mol
Surface area13290 Å2
MethodPISA
2
A: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9332
Polymers35,3251
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-5 kcal/mol
Surface area13030 Å2
MethodPISA
3
B: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9332
Polymers35,3251
Non-polymers6071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-5 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.223, 56.375, 108.445
Angle α, β, γ (deg.)90.000, 91.106, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TIGR04348 family glycosyltransferase


Mass: 35325.277 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: JF629_18585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A952K6X5
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 810 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 291.153 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 20000, 0.1M Hepes/NaOH pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.8929
pseudo-merohedral22-L, K, H20.1071
ReflectionResolution: 1.88→48.85 Å / Num. obs: 106627 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 15.2
Reflection shellResolution: 1.88→1.91 Å / Num. unique obs: 5198 / CC1/2: 0.771

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Processing

Software
NameVersionClassification
Blu-Ice5.8.0267data collection
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→48.848 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.626 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.025
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2149 4962 4.655 %
Rwork0.1865 101626 -
all0.188 --
obs-106588 94.183 %
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: 27.259 Å2
Baniso -1Baniso -2Baniso -3
1-3.959 Å20 Å26.614 Å2
2---11.483 Å2-0 Å2
3---7.524 Å2
Refinement stepCycle: LAST / Resolution: 1.88→48.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7223 0 117 810 8150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137488
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177180
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.63710205
X-RAY DIFFRACTIONr_angle_other_deg1.4181.57616399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1835957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25319.806413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1331585
X-RAY DIFFRACTIONr_chiral_restr0.0890.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028607
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021783
X-RAY DIFFRACTIONr_nbd_refined0.2070.21570
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.26706
X-RAY DIFFRACTIONr_nbtor_refined0.1550.23495
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.23910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2624
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1750.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.214
X-RAY DIFFRACTIONr_nbd_other0.1380.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1830.215
X-RAY DIFFRACTIONr_mcbond_it2.6662.6753846
X-RAY DIFFRACTIONr_mcbond_other2.6662.6753845
X-RAY DIFFRACTIONr_mcangle_it3.4843.9994797
X-RAY DIFFRACTIONr_mcangle_other3.4843.9994798
X-RAY DIFFRACTIONr_scbond_it3.3162.9593642
X-RAY DIFFRACTIONr_scbond_other3.3152.9583643
X-RAY DIFFRACTIONr_scangle_it4.6984.3235408
X-RAY DIFFRACTIONr_scangle_other4.6974.3235409
X-RAY DIFFRACTIONr_lrange_it6.47933.5688379
X-RAY DIFFRACTIONr_lrange_other6.34532.9348181
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.8920.3111000.2351900X-RAY DIFFRACTION24.0414
1.892-1.9440.3094240.2787793X-RAY DIFFRACTION101.3319
1.944-20.2833380.2077473X-RAY DIFFRACTION98.8234
2-2.0620.2632610.2027298X-RAY DIFFRACTION99.5916
2.062-2.1290.2463430.1997060X-RAY DIFFRACTION99.3691
2.129-2.2040.2192680.1936908X-RAY DIFFRACTION99.6113
2.204-2.2870.263480.2166548X-RAY DIFFRACTION99.5381
2.287-2.3810.2452940.1876412X-RAY DIFFRACTION100.4945
2.381-2.4860.2083140.1816089X-RAY DIFFRACTION99.2867
2.486-2.6080.2183220.195789X-RAY DIFFRACTION99.4305
2.608-2.7490.2163100.185511X-RAY DIFFRACTION100.1204
2.749-2.9150.1912420.1815296X-RAY DIFFRACTION99.8558
2.915-3.1160.2382140.1894990X-RAY DIFFRACTION99.7317
3.116-3.3660.212200.1924599X-RAY DIFFRACTION99.7516
3.366-3.6870.2272360.1884218X-RAY DIFFRACTION99.1982
3.687-4.1210.1712060.1663865X-RAY DIFFRACTION100.3204
4.121-4.7580.1611880.153404X-RAY DIFFRACTION99.667
4.758-5.8240.1961690.1712893X-RAY DIFFRACTION99.8695
5.824-8.2250.221150.1912301X-RAY DIFFRACTION100.7927
8.225-48.840.184500.1831279X-RAY DIFFRACTION96.6545

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