[English] 日本語
Yorodumi
- PDB-1fg5: CRYSTAL STRUCTURE OF BOVINE ALPHA-1,3-GALACTOSYLTRANSFERASE CATAL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fg5
TitleCRYSTAL STRUCTURE OF BOVINE ALPHA-1,3-GALACTOSYLTRANSFERASE CATALYTIC DOMAIN.
ComponentsN-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE
KeywordsTRANSFERASE / ALPHA BETA ALPHA PROTEIN / NUCLEOTIDE BINDING PROTEIN / ROSSMANN FOLD
Function / homology
Function and homology information


N-acetyllactosaminide 3-alpha-galactosyltransferase / N-acetyllactosaminide 3-alpha-galactosyltransferase activity / Golgi cisterna / : / Golgi cisterna membrane / : / glycosyltransferase activity / vesicle / carbohydrate metabolic process / Golgi apparatus / metal ion binding
Similarity search - Function
Glycosyl transferase, family 6 / Glycosyltransferase family 6 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
N-acetyllactosaminide alpha-1,3-galactosyltransferase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsGastinel, L.N. / Bignon, C. / Shaper, J.H. / Joziasse, D.H.
CitationJournal: EMBO J. / Year: 2001
Title: Bovine alpha1,3-galactosyltransferase catalytic domain structure and its relationship with ABO histo-blood group and glycosphingolipid glycosyltransferases.
Authors: Gastinel, L.N. / Bignon, C. / Misra, A.K. / Hindsgaul, O. / Shaper, J.H. / Joziasse, D.H.
History
DepositionJul 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
N: N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)36,9091
Polymers36,9091
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.67, 95.67, 112.93
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein N-ACETYLLACTOSAMINIDE ALPHA-1,3-GALACTOSYLTRANSFERASE / 13GALT / ALPHA-1 / 3-GALACTOSYLTRANSFERASE


Mass: 36908.566 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Description: CALF THYMUS / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P14769, EC: 2.4.1.151
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.85 % / Description: 0.9796 peak, 0.9800 inflection, 0.9324 remote
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: cacodylate, magnesium chloride, sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110-20 mg/mlprotein1drop
220 mMTris1drop
32 mM1dropMnCl2
410 mMUMP1drop
5500 mM1dropNaCl
61.3-1.6 Msodium acetate1reservoir
750 mMcacodylate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9796, 0.9800, 0.9324
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Sep 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.981
30.93241
ReflectionResolution: 2.8→36.5 Å / Num. all: 42677 / Num. obs: 11867 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.12 / % possible all: 95.7
Reflection shell
*PLUS
% possible obs: 95.7 %

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→36.5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS, Brunger et al
Details: maximum likelihood target using amplitudes and phase probability distribution
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1128 -RANDOM
Rwork0.237 ---
all0.298 42677 --
obs0.28 11867 88.1 %-
Refinement stepCycle: LAST / Resolution: 2.8→36.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2307 0 0 43 2350
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 36.5 Å / σ(F): 0 / Rfactor obs: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

+
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