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- PDB-6su6: Complex between a UDP-glucosyltransferase from Polygonum tinctori... -

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Basic information

Entry
Database: PDB / ID: 6su6
TitleComplex between a UDP-glucosyltransferase from Polygonum tinctorium capable of glucosylating indoxyl and UDP-glucose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / UDPglucose GT-B Glucosyltransferase Indigo
Function / homologyUDP-glycosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / metal ion binding / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Glycosyltransferase
Function and homology information
Biological speciesPersicaria tinctoria (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFredslund, F. / Teze, D. / Svensson, B. / Adams, P.D. / Welner, D.H.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0025660 Denmark
Novo Nordisk FoundationNNF10CC1016517 Denmark
CitationJournal: Acs Catalysis / Year: 2021
Title: O-/N-/S-Specificity in Glycosyltransferase Catalysis: From Mechanistic Understanding to Engineering
Authors: Teze, D. / Coines, J. / Fredslund, F. / Dubey, K.D. / Bidart, G.N. / Adams, P.D. / Dueber, J.E. / Svensson, B. / Rovira, C. / Welner, D.H.
History
DepositionSep 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1774
Polymers109,0442
Non-polymers1,1332
Water2,198122
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0882
Polymers54,5221
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0882
Polymers54,5221
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.240, 174.170, 48.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Glycosyltransferase


Mass: 54522.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Persicaria tinctoria (plant) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A2R2JFJ4, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2M MgCl2, 0.1M HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2016
RadiationMonochromator: SINGLE CRYSTAL, CYLINDRICALLY BENT, SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976484 Å / Relative weight: 1
ReflectionResolution: 2.4→57.25 Å / Num. obs: 40705 / % possible obs: 98.76 % / Observed criterion σ(F): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 47.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1059 / Net I/σ(I): 17.13
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.154 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 3679 / CC1/2: 0.657 / % possible all: 90.96

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
xia20.4data reduction
xia20.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nlm

5nlm


Resolution: 2.4→57.25 Å / SU ML: 0.3408 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6586
RfactorNum. reflection% reflection
Rfree0.2632 2037 5 %
Rwork0.2305 --
obs0.2322 40702 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 78.69 Å2
Refinement stepCycle: LAST / Resolution: 2.4→57.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7080 0 72 122 7274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00297327
X-RAY DIFFRACTIONf_angle_d0.58529974
X-RAY DIFFRACTIONf_chiral_restr0.04091134
X-RAY DIFFRACTIONf_plane_restr0.0041283
X-RAY DIFFRACTIONf_dihedral_angle_d12.36274394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.36221140.31712257X-RAY DIFFRACTION87.88
2.46-2.520.36241260.31032532X-RAY DIFFRACTION98.81
2.52-2.590.321250.2972582X-RAY DIFFRACTION99.56
2.59-2.660.32541190.29852569X-RAY DIFFRACTION99.48
2.66-2.750.3661350.30252549X-RAY DIFFRACTION99.55
2.75-2.850.29241440.26742583X-RAY DIFFRACTION99.71
2.85-2.960.29841470.25662553X-RAY DIFFRACTION99.82
2.96-3.090.25591440.25712558X-RAY DIFFRACTION99.93
3.09-3.260.28631360.26732602X-RAY DIFFRACTION99.89
3.26-3.460.29921530.25722591X-RAY DIFFRACTION99.71
3.46-3.730.31091550.25082545X-RAY DIFFRACTION98.5
3.73-4.10.22241370.21292589X-RAY DIFFRACTION99.16
4.1-4.70.19681190.17662644X-RAY DIFFRACTION100
4.7-5.920.25131280.19082696X-RAY DIFFRACTION100
5.92-57.250.22521550.20432815X-RAY DIFFRACTION99.76
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)
14.620190153390.323217267678-0.5499980999091.209625184640.4615190674581.260622698150.0780824606252-0.0126877628996-0.287017273097-0.0475971025803-0.0217205152154-0.06191071864070.134692977870.02084160469460.002258293113490.2952351753820.00527403958346-0.03501761832130.302509643134-0.01924647421480.137790739448-29.839961186140.3427081515-0.640403934687
21.448414264580.617406365831-0.266028795590.601030363532-0.2254744314580.795810745596-0.1729227119920.743938698651.03870873599-0.3515220704150.5174811882380.147426179552-0.1745004090740.4077553808910.2109167254060.3365049897020.02070280883170.009770939552890.418586010712-0.07830390768310.382735587407-25.135544579253.8292886704-6.75929245798
35.338971156470.03712366146690.2651630858630.8019359458150.06860710692140.6567607667860.127856634436-0.4088824137590.6853187980520.01463241226040.00737530020812-0.109819425990.01206424196340.111890885667-0.002658509587630.342508542864-0.02801710221370.03241903091360.393843724018-0.08764816429540.332388406965-7.5811525242352.83378993533.63602255741
42.755007696630.5228603673931.420150701043.194504151850.499471694033.04234205519-0.320106313240.3770462258381.09359839510.419397097426-0.3575778814380.918572973084-0.804197464203-0.473091983372-0.8808730364420.6284069272910.01922908816080.008830839092670.181816067742-0.08092064807850.825803412299-44.57859937982.256473052918.921727928
50.1145615210660.11210963958-1.356438763940.550533849043-0.03720634958611.279051376360.01014039630130.2073249270740.370707951024-0.236238442046-0.0304775704314-1.05142771905-0.8875658830220.4304813884810.08192190416561.0168036347-0.279904509477-0.1553745576270.7737041401880.08657832193311.46769682855-16.284523478795.57323061159.38782586133
61.589038140110.6870292515190.2873117033671.701642188020.577710416152.31885028608-0.2080360950290.6003860045680.06846412786070.9318526324930.330679659863-0.686423032431-0.4090022188040.5544097660030.6658716742040.844483283235-0.167260351937-0.3050815315480.5036331695760.06860186116570.924808494137-23.339435467785.679356564723.7192186406
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 224 )
2X-RAY DIFFRACTION2chain 'A' and (resid 225 through 261 )
3X-RAY DIFFRACTION3chain 'A' and (resid 262 through 476 )
4X-RAY DIFFRACTION4chain 'B' and (resid 8 through 243 )
5X-RAY DIFFRACTION5chain 'B' and (resid 244 through 350 )
6X-RAY DIFFRACTION6chain 'B' and (resid 351 through 476 )

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