[English] 日本語
Yorodumi
- PDB-4gbp: Crystal Structure of BBBB+UDP+Gal at pH 10 with MPD as the cryopr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gbp
TitleCrystal Structure of BBBB+UDP+Gal at pH 10 with MPD as the cryoprotectant
ComponentsHisto-blood group ABO system transferase
KeywordsTRANSFERASE / MANGANESE / ABO ROSSMANN FOLD / RETAINING GLYCOSYLTRANSFERASE / GLYCOPROTEIN / BLOOD GROUP ANTIGEN / METAL-BINDING
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 / hexosyltransferase activity / : / Golgi cisterna membrane / : / 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 / hexosyltransferase activity / : / Golgi cisterna membrane / : / antigen binding / manganese ion binding / vesicle / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / extracellular region / metal ion binding / membrane
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
beta-D-galactopyranose / : / URIDINE-5'-DIPHOSPHATE / 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: 2.15 Å
AuthorsJohal, A.R. / Alfaro, J.A. / Blackler, R.J. / Schuman, B. / Borisova, S.N. / Evans, S.V.
CitationJournal: Glycobiology / Year: 2014
Title: pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state.
Authors: Johal, A.R. / Blackler, R.J. / Alfaro, J.A. / Schuman, B. / Borisova, S. / Evans, S.V.
History
DepositionJul 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9585
Polymers34,1381
Non-polymers8194
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histo-blood group ABO system transferase
hetero molecules

A: Histo-blood group ABO system transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,91610
Polymers68,2772
Non-polymers1,6398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7320 Å2
ΔGint-43 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.189, 150.769, 79.397
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Histo-blood group ABO system transferase


Mass: 34138.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABO / Plasmid: PCW DELTA 1AC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD
References: UniProt: H6A2X0, UniProt: P16442*PLUS, fucosylgalactoside 3-alpha-galactosyltransferase
#2: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 10
Details: 1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM glycine, 30 mM sodium acetate with 20% MPD as cryoprotectant, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 10, 2012 / Details: OSMIC BLUE MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 17468 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.15-2.196.90.4831100
2.19-2.236.90.4231100
2.23-2.276.90.41100
2.27-2.326.90.3841100
2.32-2.376.90.3691100
2.37-2.426.90.3651100
2.42-2.4870.3041100
2.48-2.5570.2881100
2.55-2.626.90.2551100
2.62-2.7170.2211100
2.71-2.8170.1991100
2.81-2.9270.1731100
2.92-3.0570.1441100
3.05-3.2170.1161100
3.21-3.4170.0881100
3.41-3.686.90.0761100
3.68-4.056.90.0651100
4.05-4.636.80.0561100
4.63-5.836.60.0541100
5.83-4060.051199.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LZ7

1lz7


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.513 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2253 881 5 %RANDOM
Rwork0.15955 ---
obs0.16294 16566 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2283 0 50 156 2489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022400
X-RAY DIFFRACTIONr_bond_other_d0.0010.022298
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.973266
X-RAY DIFFRACTIONr_angle_other_deg0.93.0025206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08422.743113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28715394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0771519
X-RAY DIFFRACTIONr_chiral_restr0.1070.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02584
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 55 -
Rwork0.17 1089 -
obs--98.28 %

+
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