[English] 日本語
Yorodumi
- PDB-6bjj: Human ABO(H) blood group glycosyltransferase GTB D302A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bjj
TitleHuman ABO(H) blood group glycosyltransferase GTB D302A mutant
ComponentsABO blood group (Transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)
KeywordsTRANSFERASE / Blood group transferases / glycosyltransferases / enzymes
Function / homology
Function and homology information


glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / ABO blood group biosynthesis / fucosylgalactoside 3-alpha-galactosyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / hexosyltransferase activity / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding ...glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase activity / ABO blood group biosynthesis / fucosylgalactoside 3-alpha-galactosyltransferase activity / fucosylgalactoside 3-alpha-galactosyltransferase / glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / hexosyltransferase activity / lipid glycosylation / Golgi cisterna membrane / protein glycosylation / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region / membrane => GO:0016020
Similarity search - Function
Glycosyltransferase family 6 / Glycosyl transferase, 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
ABO blood group (Transferase A, alpha 1-3-N-acetylgalactosaminyltransferase; transferase B, alpha 1-3-galactosyltransferase) / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsGagnon, S.M.L. / Legg, M.S.G. / Evans, S.V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-77655 Canada
CitationJournal: Glycobiology / Year: 2018
Title: Conserved residues Arg188 and Asp302 are critical for active site organization and catalysis in human ABO(H) blood group A and B glycosyltransferases.
Authors: Gagnon, S.M.L. / Legg, M.S.G. / Polakowski, R. / Letts, J.A. / Persson, M. / Lin, S. / Zheng, R.B. / Rempel, B. / Schuman, B. / Haji-Ghassemi, O. / Borisova, S.N. / Palcic, M.M. / Evans, S.V.
History
DepositionNov 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ABO blood group (Transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)


Theoretical massNumber of molelcules
Total (without water)34,2421
Polymers34,2421
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13760 Å2
2
A: ABO blood group (Transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)

A: ABO blood group (Transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase)


Theoretical massNumber of molelcules
Total (without water)68,4832
Polymers68,4832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4730 Å2
ΔGint-25 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.690, 150.320, 78.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein ABO blood group (Transferase A, alpha 1-3-N-acetylgalactosaminyltransferase transferase B, alpha 1-3-galactosyltransferase) / ABO blood group (Transferase A / alpha 1-3-N-acetylgalactosaminyltransferase / transferase B / ...ABO blood group (Transferase A / alpha 1-3-N-acetylgalactosaminyltransferase / transferase B / alpha 1-3-galactosyltransferase)


Mass: 34241.547 Da / Num. of mol.: 1 / Fragment: UNP residues 54-344 / Mutation: D302A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli) / References: UniProt: D3HIC2, UniProt: P16442*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 277 K / Method: small tubes
Details: Spontaneous crystals were recovered from concentrated stocks of GTB/D302A (68 mg/mL) stored in 50 mM MOPS, pH 7.00, 0.1 M sodium chloride, 1 mM DTT, 5 mM manganese chloride, and kept at 277 K.

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→19.89 Å / Num. obs: 55649 / % possible obs: 99.5 % / Redundancy: 4.28 % / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.029 / Χ2: 0.99 / Net I/σ(I): 21.1 / Num. measured all: 239861 / Scaling rejects: 1800
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsΧ2Rejects% possible all
1.45-1.53.450.3033.61920355401.22104100
1.5-1.563.550.2384.31972755291.15104100
1.56-1.633.680.1955.12034955111.149699.9
1.63-1.723.850.1466.62144655301.04134100
1.72-1.834.130.1168.32321155720.97185100
1.83-1.974.610.09111.42578055510.91179100
1.97-2.174.750.06515.62673855990.87119100
2.17-2.484.870.0425.92738255960.8913299.9
2.48-3.124.930.02639.42784556070.8719899.2
3.12-19.894.920.01769.7281805614154996.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
d*TREK9.4SSIdata scaling
PDB_EXTRACT3.2data extraction
CrystalCleardata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LZ7

1lz7


Resolution: 1.45→75.16 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.992 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 2825 5.1 %RANDOM
Rwork0.1838 ---
obs0.1846 52822 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.58 Å2 / Biso mean: 22.236 Å2 / Biso min: 13.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--0.39 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.45→75.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2131 0 0 266 2397
Biso mean---34.34 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192216
X-RAY DIFFRACTIONr_bond_other_d0.0020.022049
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9493021
X-RAY DIFFRACTIONr_angle_other_deg0.95234730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1935264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82222.885104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99815357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7371516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 206 -
Rwork0.359 3881 -
all-4087 -
obs--99.93 %

+
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