[English] 日本語
Yorodumi
- PDB-4wlz: Crystal structure of mouse Xyloside xylosyltransferase 1 complexe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wlz
TitleCrystal structure of mouse Xyloside xylosyltransferase 1 complexed with manganese and UDP
ComponentsXyloside xylosyltransferase 1
KeywordsTRANSFERASE / glycosyltransferase
Function / homology
Function and homology information


xylosyl alpha-1,3-xylosyltransferase / xylosyl alpha-1,3-xylosyltransferase activity / UDP-xylosyltransferase activity / O-glycan processing / manganese ion binding / endoplasmic reticulum membrane / magnesium ion binding
Similarity search - Function
Xyloside xylosyltransferase 1 / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Xyloside xylosyltransferase 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.03 Å
AuthorsYu, H. / Li, H.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism.
Authors: Yu, H. / Takeuchi, M. / LeBarron, J. / Kantharia, J. / London, E. / Bakker, H. / Haltiwanger, R.S. / Li, H. / Takeuchi, H.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xyloside xylosyltransferase 1
B: Xyloside xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6057
Polymers70,5912
Non-polymers1,0145
Water0
1
A: Xyloside xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8514
Polymers35,2961
Non-polymers5553
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xyloside xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7553
Polymers35,2961
Non-polymers4592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Xyloside xylosyltransferase 1
hetero molecules

B: Xyloside xylosyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6057
Polymers70,5912
Non-polymers1,0145
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z+1/31
Buried area4510 Å2
ΔGint-61 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.662, 89.662, 154.987
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Xyloside xylosyltransferase 1 / UDP-xylose:alpha-xyloside alpha-1 / 3-xylosyltransferase


Mass: 35295.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Xxylt1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: Q3U4G3, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20 mM HEPES, 1.5 M Li2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.03→50 Å / Num. obs: 14615 / % possible obs: 99.3 % / Redundancy: 9 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.7
Reflection shellResolution: 3.03→3.14 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.7 / % possible all: 95

-
Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementResolution: 3.03→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / ESU R Free: 0.525 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28816 726 5 %RANDOM
Rwork0.23032 ---
obs0.23309 13780 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.433 Å2
Baniso -1Baniso -2Baniso -3
1-1.89 Å20.95 Å20 Å2
2--1.89 Å20 Å2
3----2.84 Å2
Refinement stepCycle: 1 / Resolution: 3.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 57 0 4804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.024950
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9621.9536716
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6725571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51623.306248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81615818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5351530
X-RAY DIFFRACTIONr_chiral_restr0.0630.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213786
X-RAY DIFFRACTIONr_gen_planes_other
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: 3.027→3.106 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 64 -
Rwork0.336 942 -
obs--93.41 %

+
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