[English] 日本語
Yorodumi
- PDB-9omn: WrtF fucosyltransferase - GDP-2-deoxy-2-fluoro-beta-L-fucose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9omn
TitleWrtF fucosyltransferase - GDP-2-deoxy-2-fluoro-beta-L-fucose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / inhibitor / metal-independent / GT-A / O-antigen
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / hexosyltransferase activity / Nucleotide-diphospho-sugar transferases / : / GLYCINE / PHOSPHATE ION / Glycosyltransferase
Function and homology information
Biological speciesRhizobium tropici CIAT 899 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsForrester, T.J.B. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-07113 Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: WrtF from Rhizobium tropici CIAT 899 is a GT-A fold fucosyltransferase that binds its donor nonproductively.
Authors: Forrester, T.J.B. / Lin, S. / Lowary, T.L. / Kimber, M.S.
History
DepositionMay 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,32616
Polymers61,0272
Non-polymers2,30014
Water1,08160
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7479
Polymers30,5131
Non-polymers1,2338
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5807
Polymers30,5131
Non-polymers1,0666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.530, 124.330, 45.770
Angle α, β, γ (deg.)90.000, 93.950, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Glycosyltransferase


Mass: 30513.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminally truncated / Source: (gene. exp.) Rhizobium tropici CIAT 899 (bacteria) / Cell: bacterial / Gene: GXW80_17485 / Plasmid: pET28a / Cell (production host): bacterial / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6P1C6J0

-
Non-polymers , 5 types, 74 molecules

#2: Chemical ChemComp-A1CCU / GDP-2-deoxy-2-fluoro-beta-L-fucose


Mass: 591.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24FN5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM ammonium sulfate, 100 mM HEPES pH 7.5, 35% poly (acrylic acid sodium salt) 2100

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.181 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 2.07→45.66 Å / Num. obs: 29467 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 9.1
Reflection shellResolution: 2.3→2.382 Å / Mean I/σ(I) obs: 1.92 / Num. unique obs: 2115 / CC1/2: 0.731

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.66 Å / SU ML: 0.3048 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.2714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 2872 6.78 %
Rwork0.2104 39505 -
obs0.2137 21529 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 136 60 4263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264286
X-RAY DIFFRACTIONf_angle_d0.54395828
X-RAY DIFFRACTIONf_chiral_restr0.0437664
X-RAY DIFFRACTIONf_plane_restr0.0041736
X-RAY DIFFRACTIONf_dihedral_angle_d13.85971521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.39871270.36341820X-RAY DIFFRACTION99.69
2.34-2.380.39791450.33511893X-RAY DIFFRACTION99.71
2.38-2.420.32971320.32921956X-RAY DIFFRACTION99.95
2.42-2.470.32491260.30581805X-RAY DIFFRACTION99.54
2.47-2.520.35031460.31791915X-RAY DIFFRACTION99.61
2.52-2.570.3691420.27261918X-RAY DIFFRACTION99.71
2.57-2.630.31451360.2731800X-RAY DIFFRACTION99.79
2.63-2.70.32341370.26611937X-RAY DIFFRACTION99.62
2.7-2.770.26081290.2411854X-RAY DIFFRACTION99.6
2.77-2.850.3361390.23861891X-RAY DIFFRACTION99.8
2.85-2.950.25351290.22661893X-RAY DIFFRACTION99.7
2.95-3.050.26141450.22371904X-RAY DIFFRACTION99.76
3.05-3.170.33441250.20931855X-RAY DIFFRACTION99.75
3.17-3.320.21031380.19541887X-RAY DIFFRACTION99.75
3.32-3.490.20991420.18061878X-RAY DIFFRACTION99.7
3.49-3.710.2421240.19111877X-RAY DIFFRACTION99.8
3.71-40.20781310.1721926X-RAY DIFFRACTION99.81
4-4.40.19961470.161882X-RAY DIFFRACTION100
4.4-5.030.25941490.17431876X-RAY DIFFRACTION99.9
5.03-6.340.26751440.21231866X-RAY DIFFRACTION99.41
6.34-45.660.2261390.19231872X-RAY DIFFRACTION99.55
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)
13.528219097710.00976012080039-0.664829478694.91797347999-0.896516139223.54400866796-0.0358400973503-0.3138210905110.19521523310.6799795164670.1507429341560.447478576087-0.147970691626-0.153859960133-0.08657891727970.5390991130580.0163979245820.1786269100990.241120379485-0.01891086033430.481500713668-17.692636781-11.090923754-1.09007903787
23.766805518-0.734446847627-1.596320142042.900854210160.8886477950433.10728904430.02276360834660.1876474357990.0562113200896-0.6328619680910.115852066955-0.640706964873-0.1810395120240.398288974678-0.1227719797220.626750829082-0.07454148422120.2222706963820.350429936998-0.04045663706810.5336448096430.503909831737-15.8401318811-16.5414457835
32.514779408160.139758506088-1.023951202284.85106583660.7475617153964.548946217550.04795725076960.0855307515498-0.319801377315-0.6770184281520.195002087904-1.244651328190.03954358411050.469897303901-0.2159340346430.6606572539180.05279022180950.3038411566640.333490322038-0.0134866391230.755638848137-0.174924155211-49.2285967658-18.5411521594
45.10369470546-0.5820054100581.418571054855.745403643991.191126845383.958050535-0.131333059341-0.00993303038476-0.7599803228730.153665517558-0.101246101825-0.07044929915910.777217407663-0.1573777899440.2244869675330.6554963611990.03397626827330.1963074966150.258323212801-0.01593105268870.44892167851-10.4650485339-57.1130238097-10.98462822
53.08069831369-0.0863293882646-0.6833501209434.34289850245-1.815136554463.36976852321-0.01798580565420.109322293262-0.1670583360351.20171414044-0.0570992409190.2797074893920.218302830135-0.117723066744-0.007543075693320.4820253542730.05052996733080.05835071451630.1711963739530.007646520332460.329945165978-14.7382600784-45.9595216083-4.39041891946
65.926718890350.610551855041-0.3320898608490.204621698994-0.8573610544254.769323612440.111036135963-0.7238433645270.05311491383650.0832093450137-0.202477050987-0.3058466630460.0714957534564-0.003387324057360.06890313933870.7387244741020.07162188662870.1337344987950.369231302822-0.07565518592050.538845295701-9.34206061091-52.7222826715-2.70633915515
79.29930969817-0.245851283741-2.010943125241.085591404750.5941336462614.815039719170.0756699195445-0.4693567727170.9005582290560.638213337090.2119042711140.00516092513849-0.1033295865990.102274033826-0.1348996083370.7467484243060.08177701834680.1460935049290.289485697482-0.03339871256580.51230018254-15.7919613836-34.73778505176.85204360935
86.711106635412.624761196661.267067684256.34867005292-2.909083722322.614328386570.298393806186-1.47771798273-0.9824950862521.52068110167-0.446563552638-0.355342178727-0.1892970501490.5109603055110.3907900774571.343027034740.0604652305490.6436637277820.663707065345-0.1508378550420.885164622306-24.9023220545-37.014351564815.4473782368
91.53827319161.84970863289-1.993763553932.33295527174-1.732209582324.56539535765-0.4153464770320.2730567937810.02042445696420.8091648963720.02636798373331.181957534450.784933392325-0.6178737963980.2926610750051.157823091670.0570606569540.5606434775490.5630390322540.02678885077140.952019730614-32.8300453368-42.945930750211.163505502
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 97 )AA3 - 971 - 95
22chain 'A' and (resid 98 through 302 )AA - C98 - 30296 - 257
33chain 'B' and (resid 3 through 78 )BE3 - 781 - 76
44chain 'B' and (resid 79 through 119 )BE79 - 11977 - 117
55chain 'B' and (resid 120 through 176 )BE120 - 176118 - 174
66chain 'B' and (resid 177 through 200 )BE177 - 200175 - 195
77chain 'B' and (resid 201 through 231 )BE201 - 231196 - 226
88chain 'B' and (resid 232 through 250 )BE232 - 250227 - 244
99chain 'B' and (resid 251 through 278 )BE251 - 278245 - 272

+
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