[English] 日本語
Yorodumi
- PDB-2pgy: GTB C209A, no Hg -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pgy
TitleGTB C209A, no Hg
ComponentsGlycoprotein-fucosylgalactoside alpha-galactosyltransferase
KeywordsTRANSFERASE / GTB / C209A / Glycosyltransferase / ABO(H) / Blood Group / H-antigen / Rossmann fold
Function / homology
Function and homology information


fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding ...fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase activity / ABO blood group biosynthesis / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region
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
Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLetts, J.A. / Schuman, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: The effect of heavy atoms on the conformation of the active-site polypeptide loop in human ABO(H) blood-group glycosyltransferase B.
Authors: Letts, J.A. / Persson, M. / Schuman, B. / Borisova, S.N. / Palcic, M.M. / Evans, S.V.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoprotein-fucosylgalactoside alpha-galactosyltransferase


Theoretical massNumber of molelcules
Total (without water)33,9771
Polymers33,9771
Non-polymers00
Water2,144119
1
A: Glycoprotein-fucosylgalactoside alpha-galactosyltransferase

A: Glycoprotein-fucosylgalactoside alpha-galactosyltransferase


Theoretical massNumber of molelcules
Total (without water)67,9542
Polymers67,9542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4870 Å2
ΔGint-28 kcal/mol
Surface area22840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)53.390, 151.850, 80.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Histo-blood group B transferase / B transferase


Mass: 33977.207 Da / Num. of mol.: 1 / Fragment: GTB / Mutation: C209A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: pcWDeltaLac / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P16442, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.39 Å3/Da / Density % sol: 48.58 %

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 27, 2006 / Details: Osmic
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 4.43 % / Av σ(I) over netI: 11.5 / Number: 57000 / Rmerge(I) obs: 0.075 / Χ2: 0.98 / D res high: 2.39 Å / D res low: 19.5 Å / Num. obs: 12774 / % possible obs: 96
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
5.1219.592.20.0360.784.3521
4.085.1296.30.0410.724.4332
3.574.0896.90.0560.74.4127
3.243.5796.90.0760.894.4436
3.013.2496.70.1110.94.4330
2.833.0196.90.151.024.4351
2.692.8396.60.1921.184.4750
2.572.6996.30.2181.164.4646
2.482.5796.20.2291.124.4557
2.392.4895.60.2731.324.4379
ReflectionResolution: 2.39→19.5 Å / Num. obs: 12774 / % possible obs: 96 % / Redundancy: 4.43 % / Rmerge(I) obs: 0.075 / Χ2: 0.98 / Net I/σ(I): 11.5 / Scaling rejects: 429
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.39-2.484.430.2733.8567012631.3295.6
2.48-2.574.450.2294.4564312551.1296.2
2.57-2.694.460.2184.7565812591.1696.3
2.69-2.834.470.1925.6571312681.1896.6
2.83-3.014.430.156.1566012661.0296.9
3.01-3.244.430.1118.5567512740.996.7
3.24-3.574.440.07612.5576012890.8996.9
3.57-4.084.410.05616.9573512940.796.9
4.08-5.124.430.04123.1577112960.7296.3
5.12-19.54.350.03628.5571513100.7892.2

-
Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GTB

Resolution: 2.39→19.5 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.933 / SU ML: 0.164 / Isotropic thermal model: GTB / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.382 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 630 4.9 %RANDOM
Rwork0.168 ---
obs0.172 12746 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2--0.39 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.39→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 0 119 2340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222283
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.9513102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4115270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25222.752109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09815378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.511518
X-RAY DIFFRACTIONr_chiral_restr0.0920.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021749
X-RAY DIFFRACTIONr_nbd_refined0.1930.2864
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.213
X-RAY DIFFRACTIONr_mcbond_it0.8351.51394
X-RAY DIFFRACTIONr_mcangle_it1.38422213
X-RAY DIFFRACTIONr_scbond_it1.87631017
X-RAY DIFFRACTIONr_scangle_it3.0194.5889
LS refinement shellResolution: 2.39→2.451 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 44 -
Rwork0.218 879 -
obs-923 95.06 %

+
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