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- PDB-8jjn: Structure of SenB in complex with UDP-Glc and PO4- at 1.98 Angstr... -

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Basic information

Entry
Database: PDB / ID: 8jjn
TitleStructure of SenB in complex with UDP-Glc and PO4- at 1.98 Angstroms resolution
ComponentsTIGR04348 family glycosyltransferase
KeywordsTRANSFERASE / Complex with UDP-Glc and PO4-
Function / homologyPutative glycosyltransferase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE / TIGR04348 family glycosyltransferase
Function and homology information
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsHuang, W. / Long, F.
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-Glc and PO4- at 1.98 Angstroms resolution
Authors: Huang, W. / Long, F.
History
DepositionMay 31, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)107,0869
Polymers105,1023
Non-polymers1,9846
Water7,800433
1
C: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6953
Polymers35,0341
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-5 kcal/mol
Surface area13490 Å2
MethodPISA
2
A: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6953
Polymers35,0341
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-13 kcal/mol
Surface area12780 Å2
MethodPISA
3
B: TIGR04348 family glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6953
Polymers35,0341
Non-polymers6612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-5 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.825, 55.792, 108.076
Angle α, β, γ (deg.)90.00, 90.94, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein TIGR04348 family glycosyltransferase


Mass: 35033.938 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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 291.153 K / Method: vapor diffusion, sitting drop
Details: 20%PEG8000, 0.2M(NH4SO4, 0.1M Hepes pH 7.5,10% 2-propanol

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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: Mar 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.98→49.57 Å / Num. obs: 89982 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 28.22 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7
Reflection shellResolution: 1.98→2.01 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 575 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Blu-Icedata collection
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→48.55 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 4529 5.03 %
Rwork0.191 --
obs0.1925 89952 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7221 0 108 433 7762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087471
X-RAY DIFFRACTIONf_angle_d0.97710180
X-RAY DIFFRACTIONf_dihedral_angle_d8.1781132
X-RAY DIFFRACTIONf_chiral_restr0.0531162
X-RAY DIFFRACTIONf_plane_restr0.0111336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-20.3281340.27392835X-RAY DIFFRACTION100
2-2.030.30691600.2632800X-RAY DIFFRACTION100
2.03-2.050.28021590.2492829X-RAY DIFFRACTION100
2.05-2.080.30911140.23392867X-RAY DIFFRACTION100
2.08-2.10.26831590.23272809X-RAY DIFFRACTION100
2.1-2.130.27341670.21632831X-RAY DIFFRACTION100
2.13-2.160.27741610.2142820X-RAY DIFFRACTION100
2.16-2.20.23491550.20382771X-RAY DIFFRACTION100
2.2-2.230.2551670.19912858X-RAY DIFFRACTION100
2.23-2.270.23681550.20472801X-RAY DIFFRACTION100
2.27-2.310.23571480.19942857X-RAY DIFFRACTION100
2.31-2.350.2721230.19282873X-RAY DIFFRACTION100
2.35-2.390.24161610.19062796X-RAY DIFFRACTION100
2.39-2.440.22541450.19682859X-RAY DIFFRACTION100
2.44-2.490.25311560.19092806X-RAY DIFFRACTION100
2.49-2.550.20711420.18432862X-RAY DIFFRACTION100
2.55-2.620.26451690.18552808X-RAY DIFFRACTION100
2.62-2.690.19871380.18012876X-RAY DIFFRACTION100
2.69-2.770.22041190.18222891X-RAY DIFFRACTION100
2.77-2.860.18831580.18732793X-RAY DIFFRACTION100
2.86-2.960.25421940.19042833X-RAY DIFFRACTION100
2.96-3.080.22611320.19822879X-RAY DIFFRACTION100
3.08-3.220.24121490.19322849X-RAY DIFFRACTION100
3.22-3.390.21761420.19422862X-RAY DIFFRACTION100
3.39-3.60.19651480.18782873X-RAY DIFFRACTION100
3.6-3.870.19291170.17342889X-RAY DIFFRACTION100
3.88-4.260.21790.16792848X-RAY DIFFRACTION100
4.26-4.880.17121470.16232903X-RAY DIFFRACTION100
4.88-6.150.21051800.20182867X-RAY DIFFRACTION100
6.15-48.550.18861510.19152978X-RAY DIFFRACTION99

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