[English] 日本語
Yorodumi
- PDB-6su6: Complex between a UDP-glucosyltransferase from Polygonum tinctori... -

+
Open data


ID or keywords:

Loading...

-
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 family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more