[English] 日本語
Yorodumi
- PDB-2i7b: Structure of the naturally occuring mutant of human ABO(H) Blood ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i7b
TitleStructure of the naturally occuring mutant of human ABO(H) Blood group B glycosyltransferase: GTB/A268T
Componentsalpha 1-3-galactosyltransferase
KeywordsTRANSFERASE / glycosyltransferase / blood group / ABO allele / hybrid allele
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 / glycosyltransferase activity / protein glycosylation / antigen 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 / glycosyltransferase activity / protein glycosylation / antigen binding / manganese ion binding / vesicle / membrane => GO:0016020 / 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 / Histo-blood group ABO system transferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLetts, J.A. / Evans, S.V.
CitationJournal: Transfusion / Year: 2007
Title: Structural basis for red cell phenotypic changes in newly identified, naturally occurring subgroup mutants of the human blood group B glycosyltransferase.
Authors: Hosseini-Maaf, B. / Letts, J.A. / Persson, M. / Smart, E. / Lepennec, P.Y. / Hustinx, H. / Zhao, Z. / Palcic, M.M. / Evans, S.V. / Chester, M.A. / Olsson, M.L.
History
DepositionAug 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha 1-3-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8425
Polymers34,0391
Non-polymers8024
Water3,351186
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: alpha 1-3-galactosyltransferase
hetero molecules

A: alpha 1-3-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,68310
Polymers68,0792
Non-polymers1,6058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6040 Å2
ΔGint-225 kcal/mol
Surface area22090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.540, 148.950, 80.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein alpha 1-3-galactosyltransferase / Transferase A / alpha 1-3-N- acetylgalactosaminyltransferase / transferase B


Mass: 34039.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: pcW / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q6ISD4, UniProt: P16442*PLUS
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growDetails: 6-8 mg/ml GTB/A268T, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA), pH 7.5, 50 mM CH3COONa, pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (w/v) 2-methyl-2,4-pentanediol (MPD), 5% (w/v) glycerol, ...Details: 6-8 mg/ml GTB/A268T, 70 mM N-(2-acetamido)-2-iminodiacetic acid (ADA), pH 7.5, 50 mM CH3COONa, pH 4.6, 40 mM NaCl, 5-8 mM MnCl2, 2.5% (w/v) 2-methyl-2,4-pentanediol (MPD), 5% (w/v) glycerol, 2% (w/v) PEG 4000 and 0.3-0.5 mM

-
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 "Blue" Confocal x-ray mirrors (Osmic)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.99→20 Å / Num. all: 21947 / Num. obs: 21267 / % possible obs: 96.9 % / Redundancy: 4.86 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.9
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2128 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LZ7

1lz7


Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.664 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23063 1102 5.2 %RANDOM
Rwork0.1847 ---
obs0.18713 20163 96.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.973 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--0.61 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 4 186 2333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222206
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.953001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76822.762105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35315363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1831517
X-RAY DIFFRACTIONr_chiral_restr0.1260.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021685
X-RAY DIFFRACTIONr_nbd_refined0.2120.21013
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21508
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.221
X-RAY DIFFRACTIONr_mcbond_it1.2131.51354
X-RAY DIFFRACTIONr_mcangle_it1.80622139
X-RAY DIFFRACTIONr_scbond_it2.7743995
X-RAY DIFFRACTIONr_scangle_it4.0854.5862
LS refinement shellResolution: 1.99→2.041 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 87 -
Rwork0.234 1496 -
obs--99.25 %

+
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