[English] 日本語
Yorodumi
- PDB-8k2i: Crystal structure of Group 2 Oligosaccharide/Monosaccharide-relea... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k2i
TitleCrystal structure of Group 2 Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase NgaAt from Arabidopsis thaliana in complex with GlcNAc-thiazoline
ComponentsOligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase
KeywordsHYDROLASE / Glycoside Hydrolase
Function / homologyGlycoside hydrolase 123, C-terminal / Glycoside hydrolase 123, catalytic domain / Chem-NGT / DI(HYDROXYETHYL)ETHER / Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase
Function and homology information
Biological speciesArabidopsis thaliana x Arabidopsis lyrata (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSumida, T. / Fushinobu, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22K05398 Japan
Japan Society for the Promotion of Science (JSPS)JP20K15444 Japan
Mizutani Foundation for GlycoscienceFT100100291 Japan
CitationJournal: Nat Commun / Year: 2024
Title: Genetic and functional diversity of beta-N-acetylgalactosamine-targeting glycosidases expanded by deep-sea metagenome analysis.
Authors: Sumida, T. / Hiraoka, S. / Usui, K. / Ishiwata, A. / Sengoku, T. / Stubbs, K.A. / Tanaka, K. / Deguchi, S. / Fushinobu, S. / Nunoura, T.
History
DepositionJul 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase
A: Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,9927
Polymers145,3062
Non-polymers6865
Water4,342241
1
B: Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9783
Polymers72,6531
Non-polymers3252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23430 Å2
MethodPISA
2
A: Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0144
Polymers72,6531
Non-polymers3613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.284, 133.833, 150.723
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Oligosaccharide/Monosaccharide-releasing beta-N-acetylhexosaminidase / At1g45150 / Uncharacterized protein At1g45150


Mass: 72653.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana x Arabidopsis lyrata (thale cress)
Gene: At1g45150, F27F5.22, F27F5_22 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Y231
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO4S
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Hepes-Na pH 7.5, 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.13 Å / Num. obs: 49358 / % possible obs: 100 % / Redundancy: 13.9 % / CC1/2: 0.994 / Net I/σ(I): 7.4
Reflection shellResolution: 2.5→2.58 Å / Num. unique obs: 4468 / CC1/2: 0.684

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.71 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.2 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22989 2489 5.1 %RANDOM
Rwork0.15719 ---
obs0.16084 46789 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å2-0 Å2-0 Å2
2---3.95 Å2-0 Å2
3---1.49 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8911 0 43 241 9195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0129239
X-RAY DIFFRACTIONr_bond_other_d0.0030.0168272
X-RAY DIFFRACTIONr_angle_refined_deg2.1811.65212618
X-RAY DIFFRACTIONr_angle_other_deg0.6911.55319328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.35151119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.362570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.936101459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0910.21360
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0210475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021853
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_it6.6715.4354476
X-RAY DIFFRACTIONr_mcbond_other6.6565.4364476
X-RAY DIFFRACTIONr_mcangle_it8.8658.145589
X-RAY DIFFRACTIONr_mcangle_other8.8658.1435590
X-RAY DIFFRACTIONr_scbond_it7.8295.8584763
X-RAY DIFFRACTIONr_scbond_other7.8285.8574764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.1758.5657028
X-RAY DIFFRACTIONr_long_range_B_refined11.73769.2039867
X-RAY DIFFRACTIONr_long_range_B_other11.74969.0039837
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 174 -
Rwork0.266 3415 -
obs--99.97 %

+
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