[English] 日本語
Yorodumi
- PDB-4lw3: Crystal structure of the Drosophila beta1,4galactosyltransferase7... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lw3
TitleCrystal structure of the Drosophila beta1,4galactosyltransferase7 catalytic domain D211N single mutant enzyme complex with manganese and UDP-galactose
ComponentsBeta-4-galactosyltransferase 7
KeywordsTRANSFERASE / GT-A glycosyltransferase family / manganese and UDp-galactose / Golgi
Function / homology
Function and homology information


glycosaminoglycan-protein linkage region biosynthetic process / xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / A tetrasaccharide linker sequence is required for GAG synthesis / chondroitin sulfate proteoglycan biosynthetic process / glycosylation / heparan sulfate proteoglycan biosynthetic process / proteoglycan biosynthetic process / N-glycan processing / protein glycosylation ...glycosaminoglycan-protein linkage region biosynthetic process / xylosylprotein 4-beta-galactosyltransferase / xylosylprotein 4-beta-galactosyltransferase activity / A tetrasaccharide linker sequence is required for GAG synthesis / chondroitin sulfate proteoglycan biosynthetic process / glycosylation / heparan sulfate proteoglycan biosynthetic process / proteoglycan biosynthetic process / N-glycan processing / protein glycosylation / carbohydrate metabolic process / Golgi membrane / nucleotide binding / Golgi apparatus / metal ion binding
Similarity search - Function
Beta-1,4-galactosyltransferase / Galactosyltransferase, N-terminal / N-terminal region of glycosyl transferase group 7 / Galactosyltransferase, C-terminal / N-terminal domain of galactosyltransferase / 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
GALACTOSE-URIDINE-5'-DIPHOSPHATE / : / Beta-1,4-galactosyltransferase 7
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRamakrishnan, B. / Qasba, P.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structures of beta-1,4-Galactosyltransferase 7 Enzyme Reveal Conformational Changes and Substrate Binding.
Authors: Tsutsui, Y. / Ramakrishnan, B. / Qasba, P.K.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Sep 20, 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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-4-galactosyltransferase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9413
Polymers33,3191
Non-polymers6212
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.087, 82.087, 133.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-803-

HOH

-
Components

#1: Protein Beta-4-galactosyltransferase 7 / FI08434p


Mass: 33319.305 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 71-311 / Mutation: D221N
Source method: isolated from a genetically manipulated source
Details: Protein expressed as inclusion bodies and in vitro refolded
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: 4-galactosyltransferase-7, beta-4GalT7, beta1, beta4GalT7, beta4GalT7-RA, CG11780, Dmel_CG11780
Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9VBZ9, Transferases; Glycosyltransferases; Hexosyltransferases, xylosylprotein 4-beta-galactosyltransferase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 566.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM HEPES, 5% PEG 6K, 10% MPD, 2 mM MnCl2, 2 mM UDP-Gal, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 17, 2013 / Details: Mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29731 / % possible obs: 97 % / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Rsym value: 0.057 / Net I/σ(I): 36.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2614 / Rsym value: 0.353 / % possible all: 85.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LW6

3lw6


Resolution: 2→28.913 Å / SU ML: 0.2 / Cross valid method: Throught / σ(F): 1.33 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 1536 5.05 %random
Rwork0.174 ---
obs0.1757 26249 96.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→28.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 37 304 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072128
X-RAY DIFFRACTIONf_angle_d1.1052886
X-RAY DIFFRACTIONf_dihedral_angle_d13.417801
X-RAY DIFFRACTIONf_chiral_restr0.076308
X-RAY DIFFRACTIONf_plane_restr0.004370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06420.27341090.21742252X-RAY DIFFRACTION84
2.0642-2.1380.24021230.20032559X-RAY DIFFRACTION96
2.138-2.22360.25541240.19792613X-RAY DIFFRACTION97
2.2236-2.32470.26481480.19182595X-RAY DIFFRACTION98
2.3247-2.44720.26281340.19172637X-RAY DIFFRACTION98
2.4472-2.60040.24841530.20012607X-RAY DIFFRACTION97
2.6004-2.80110.21741480.19852631X-RAY DIFFRACTION97
2.8011-3.08270.24881230.22656X-RAY DIFFRACTION97
3.0827-3.52810.20681490.17082663X-RAY DIFFRACTION97
3.5281-4.44240.18481620.14122732X-RAY DIFFRACTION99
4.4424-28.9130.16521630.16462913X-RAY DIFFRACTION99

+
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