[English] 日本語
Yorodumi
- PDB-8k2m: Crystal structure of Group 4 Monosaccharide-releasing beta-N-acet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k2m
TitleCrystal structure of Group 4 Monosaccharide-releasing beta-N-acetylgalactosaminidase NgaP2 from Paenibacillus sp. TS12 in complex with GalNAc-thiazoline
ComponentsMonosaccharide-releasing beta-N-acetylgalactosaminidase
KeywordsHYDROLASE / Glycoside hydrolase
Function / homologyBROMIDE ION / Chem-GNL
Function and homology information
Biological speciesPaenibacillus sp. TS12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
A: Monosaccharide-releasing beta-N-acetylgalactosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8884
Polymers66,5091
Non-polymers3793
Water7,656425
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.975, 61.608, 100.453
Angle α, β, γ (deg.)90.00, 121.43, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Monosaccharide-releasing beta-N-acetylgalactosaminidase


Mass: 66508.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. TS12 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GNL / (3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol


Mass: 219.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO4S
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium Bromide, 0.1 M Bis-Tris 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: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→47.15 Å / Num. obs: 74805 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC1/2: 0.987 / Net I/σ(I): 8.8
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 3646 / CC1/2: 0.987

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→47.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.495 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 3800 5.1 %RANDOM
Rwork0.16848 ---
obs0.1698 70898 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å20.44 Å2
2--0.22 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 1.65→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4530 0 16 425 4971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124684
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164154
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.6466373
X-RAY DIFFRACTIONr_angle_other_deg0.5931.5639695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6615558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.668526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06110747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025314
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02990
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_it2.0062.2722235
X-RAY DIFFRACTIONr_mcbond_other2.0052.2722235
X-RAY DIFFRACTIONr_mcangle_it2.8223.4062792
X-RAY DIFFRACTIONr_mcangle_other2.8223.4082793
X-RAY DIFFRACTIONr_scbond_it3.4042.6012449
X-RAY DIFFRACTIONr_scbond_other3.4032.6012450
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1473.7523582
X-RAY DIFFRACTIONr_long_range_B_refined6.11328.0134912
X-RAY DIFFRACTIONr_long_range_B_other6.02526.9854850
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 273 -
Rwork0.292 5151 -
obs--97.89 %

+
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