[English] 日本語
Yorodumi
- PDB-5cmi: GTA mutant without mercury - E303D -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cmi
TitleGTA mutant without mercury - E303D
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / Human ABO(H) blood group system / Glycosyltransferase / Double turn motif / Catalytic domain
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 / : / Golgi cisterna membrane / : / 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 / : / Golgi cisterna membrane / : / 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: 1.85 Å
AuthorsGagnon, S.M.L. / Blackler, R.J.
CitationJournal: Glycobiology / Year: 2017
Title: Glycosyltransfer in mutants of putative catalytic residue Glu303 of the human ABO(H) A and B blood group glycosyltransferases GTA and GTB proceeds through a labile active site.
Authors: Blackler, R.J. / Gagnon, S.M. / Polakowski, R. / Rose, N.L. / Zheng, R.B. / Letts, J.A. / Johal, A.R. / Schuman, B. / Borisova, S.N. / Palcic, M.M. / Evans, S.V.
History
DepositionJul 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Jan 11, 2017Group: Database references
Revision 1.3Apr 19, 2017Group: Database references
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histo-blood group ABO system transferase


Theoretical massNumber of molelcules
Total (without water)34,3101
Polymers34,3101
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.510, 149.570, 78.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Histo-blood group ABO system transferase / Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N- ...Fucosylglycoprotein 3-alpha-galactosyltransferase / Fucosylglycoprotein alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase / Glycoprotein-fucosylgalactoside alpha-galactosyltransferase / Histo-blood group A transferase / A transferase / Histo-blood group B transferase / B transferase / NAGAT


Mass: 34309.582 Da / Num. of mol.: 1 / Fragment: Catalytic domain (UNP residues 64-354) / Mutation: E303D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Production host: Escherichia coli (E. coli)
References: UniProt: P16442, glycoprotein-fucosylgalactoside alpha-N-acetylgalactosaminyltransferase, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 30-40 mg/ml protein, 1% PEG (w/v) 4000, 4.5% MPD (v/v), 0.1 M ammonium sulfate, 0.07 M NaCl, 0.05 M ADA buffer, pH 7.5, 5 mM MnCl2 against a reservoir containing 2.7% (w/v) PEG 4000, 7% (v/v) ...Details: 30-40 mg/ml protein, 1% PEG (w/v) 4000, 4.5% MPD (v/v), 0.1 M ammonium sulfate, 0.07 M NaCl, 0.05 M ADA buffer, pH 7.5, 5 mM MnCl2 against a reservoir containing 2.7% (w/v) PEG 4000, 7% (v/v) MPD, 0.32 M ammonium sulfate, 0.25 M NaCl, and 0.2 M ADA pH 7.5

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→74.74 Å / Num. obs: 26045 / % possible obs: 97.4 % / Redundancy: 4.62 % / Rmerge(I) obs: 0.06 / Χ2: 0.97 / Net I/σ(I): 11.5 / Num. measured all: 121206 / Scaling rejects: 910
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.85-1.924.420.3363.41161326191.224199.8
1.92-1.994.420.2773.91168126341.174399.7
1.99-2.084.420.224.61164326271.14199.6
2.08-2.194.50.1815.61199926541.095599.4
2.19-2.334.570.1436.811931259018599
2.33-2.514.640.1178.11227326190.9311498.2
2.51-2.764.670.1019.31229226010.8714997.6
2.76-3.164.790.07131237825640.8210395.5
3.16-3.984.890.0424.41257025390.7815593.3
3.98-19.564.890.03133.81282625980.7712492.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
d*TREK9.4SSIdata scaling
PDB_EXTRACT3.15data extraction
CrystalCleardata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LZ0

1lz0


Resolution: 1.85→19.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.899 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.141 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 1310 5 %RANDOM
Rwork0.1809 ---
obs0.1834 24734 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.28 Å2 / Biso mean: 29.97 Å2 / Biso min: 16.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2--0.07 Å20 Å2
3---1.12 Å2
Refinement stepCycle: final / Resolution: 1.85→19.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 0 216 2499
Biso mean---37.81 -
Num. residues----282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192345
X-RAY DIFFRACTIONr_bond_other_d0.0010.022220
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9493187
X-RAY DIFFRACTIONr_angle_other_deg0.87135081
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9395280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95422.768112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43515382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0561519
X-RAY DIFFRACTIONr_chiral_restr0.10.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02576
X-RAY DIFFRACTIONr_mcbond_it2.2942.7981126
X-RAY DIFFRACTIONr_mcbond_other2.2582.7941125
X-RAY DIFFRACTIONr_mcangle_it3.2014.1751404
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 92 -
Rwork0.246 1848 -
all-1940 -
obs--99.74 %

+
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