[English] 日本語
Yorodumi
- PDB-5kwk: The structure of Arabidopsis thaliana FUT1 in complex with GDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kwk
TitleThe structure of Arabidopsis thaliana FUT1 in complex with GDP
ComponentsGalactoside 2-alpha-L-fucosyltransferase
KeywordsCELL ADHESION / acetyl transferase / GT37
Function / homology
Function and homology information


galactoside 2-alpha-L-fucosyltransferase activity / xyloglucan biosynthetic process / fucosyltransferase activity / cell wall biogenesis / Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / Golgi medial cisterna / cell wall organization / Golgi membrane / Golgi apparatus / protein homodimerization activity
Similarity search - Function
Xyloglucan fucosyltransferase / Xyloglucan fucosyltransferase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Galactoside 2-alpha-L-fucosyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: Plant J. / Year: 2017
Title: Structural, mutagenic and in silico studies of xyloglucan fucosylation in Arabidopsis thaliana suggest a water-mediated mechanism.
Authors: Urbanowicz, B.R. / Bharadwaj, V.S. / Alahuhta, M. / Pena, M.J. / Lunin, V.V. / Bomble, Y.J. / Wang, S. / Yang, J.Y. / Tuomivaara, S.T. / Himmel, M.E. / Moremen, K.W. / York, W.S. / Crowley, M.F.
History
DepositionJul 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references / Structure summary
Revision 1.2May 30, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galactoside 2-alpha-L-fucosyltransferase
B: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,80923
Polymers108,4472
Non-polymers2,36221
Water18,5911032
1
A: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,45112
Polymers54,2231
Non-polymers1,22711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,35811
Polymers54,2231
Non-polymers1,13510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.933, 113.103, 87.781
Angle α, β, γ (deg.)90.00, 105.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Galactoside 2-alpha-L-fucosyltransferase / / Xyloglucan alpha-(1 / 2)-fucosyltransferase / AtFUT1


Mass: 54223.488 Da / Num. of mol.: 2 / Fragment: residues 84-558
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FUT1, FT1, MUR2, At2g03220, T18E12.11 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q9SWH5, EC: 2.4.1.69

-
Non-polymers , 5 types, 1053 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1032 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7 mg/mL protein in 0.1 M MES pH 6.0 to 7.0 and 16% to 23% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54188 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 10, 2014 / Details: Helios mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54188 Å / Relative weight: 1
ReflectionResolution: 1.9→84.78 Å / Num. obs: 79818 / % possible obs: 99.8 % / Redundancy: 5.11 % / Rmerge(I) obs: 0.1343 / Net I/σ(I): 6.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.5897 / Mean I/σ(I) obs: 1.5 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementResolution: 1.9→84.78 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.897 / SU B: 14.581 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28882 3790 4.8 %RANDOM
Rwork0.22262 ---
obs0.22583 74433 97.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å2-0.27 Å2
2---1.61 Å2-0 Å2
3---2.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→84.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7183 0 150 1032 8365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0197856
X-RAY DIFFRACTIONr_bond_other_d0.0020.027251
X-RAY DIFFRACTIONr_angle_refined_deg2.1751.94810675
X-RAY DIFFRACTIONr_angle_other_deg1.415316790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215952
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41223.96351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.428151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8971532
X-RAY DIFFRACTIONr_chiral_restr0.1470.21117
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0218806
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021832
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9930.6673739
X-RAY DIFFRACTIONr_mcbond_other0.9930.6683738
X-RAY DIFFRACTIONr_mcangle_it1.7540.9914714
X-RAY DIFFRACTIONr_mcangle_other1.7540.9914715
X-RAY DIFFRACTIONr_scbond_it1.0560.8214117
X-RAY DIFFRACTIONr_scbond_other1.0550.8214117
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6691.175962
X-RAY DIFFRACTIONr_long_range_B_refined7.6089.8719392
X-RAY DIFFRACTIONr_long_range_B_other7.498.8379184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 226 -
Rwork0.335 5483 -
obs--96.71 %
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)
10.4921-0.47730.21930.9265-0.11821.1263-0.0848-0.0155-0.03140.0520.01210.0933-0.1951-0.02560.07280.25810.03320.02680.26770.00750.0226.3537.51838.387
20.3168-0.3361-0.3351.0506-0.2561.3854-0.01850.0083-0.0328-0.1154-0.0518-0.00070.18230.04310.07030.26760.01840.0650.2832-0.00770.018926.39-12.11722.35
30.262-0.3516-0.40670.75060.34690.9068-0.0458-0.0178-0.03040.02520.00860.0140.00930.01490.03730.25520.03090.05330.3076-0.00170.016323.73-9.73833.48
40.6378-0.0897-0.29870.8022-0.09940.48830.0377-0.0363-0.02740.0274-0.0556-0.0463-0.00810.08210.01790.2681-0.00180.04410.28020.00680.013133.414-25.32272.175
50.4273-0.2644-0.27421.1567-0.33750.9192-0.0096-0.0770.01980.0421-0.00320.0334-0.0617-0.05910.01280.28580.02280.05310.3163-0.04510.022310.766-6.03387.938
60.6574-0.3906-0.3580.31250.08090.64890.0411-0.05280.0413-0.0589-0.0047-0.0273-0.09710.0421-0.03640.32140.00250.07150.2878-0.02350.019520.61-6.09978.441
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 337
2X-RAY DIFFRACTION2A338 - 409
3X-RAY DIFFRACTION3A410 - 558
4X-RAY DIFFRACTION4B95 - 337
5X-RAY DIFFRACTION5B338 - 426
6X-RAY DIFFRACTION6B427 - 558

+
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