[English] 日本語
Yorodumi
- PDB-6jeb: crystal structure of a beta-N-acetylhexosaminidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jeb
Titlecrystal structure of a beta-N-acetylhexosaminidase
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / Catalyze / acetamidodeoxyhexohydrolase
Function / homology
Function and homology information


chitobiose catabolic process / beta-N-acetylgalactosaminidase activity / beta-N-acetylhexosaminidase / : / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / metal ion binding
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETAMIDE / Beta-hexosaminidase Amuc_2018
Similarity search - Component
Biological speciesAkkermansia muciniphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsChen, X. / Wang, J.C. / Liu, M.J. / Yang, W.Y. / Wang, Y.Z. / Tang, R.P. / Zhang, M.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystallographic evidence for substrate-assisted catalysis of beta-N-acetylhexosaminidas from Akkermansia muciniphila.
Authors: Chen, X. / Wang, J. / Liu, M. / Yang, W. / Wang, Y. / Tang, R. / Zhang, M.
History
DepositionFeb 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7533
Polymers53,6281
Non-polymers1242
Water13,565753
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.342, 91.342, 274.807
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-718-

HOH

21A-917-

HOH

31A-1265-

HOH

-
Components

#1: Protein Beta-N-acetylhexosaminidase


Mass: 53628.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria)
Strain: ATCC BAA-835 / Muc / Gene: Amuc_2018
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B2UP57, beta-N-acetylhexosaminidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.1M Sodium malonate, pH 7.0; 0.1 M HEPES pH 7.0; 0.5%v/v Jeffamine ED-2001 pH 7.0.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 109396 / % possible obs: 100 % / Redundancy: 27.5 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.016 / Rrim(I) all: 0.084 / Χ2: 0.953 / Net I/σ(I): 7.5 / Num. measured all: 3007998
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5529.71.048107270.9090.1941.0660.845100
1.55-1.6229.80.759107350.950.140.7720.852100
1.62-1.6929.20.545107810.9720.1020.5540.86100
1.69-1.7827.30.382107910.9860.0740.390.873100
1.78-1.8929.20.253108170.9940.0470.2580.894100
1.89-2.0429.60.157108790.9980.0290.160.926100
2.04-2.2428.10.097108810.9990.0180.0980.97399.9
2.24-2.5624.90.065109750.9990.0130.0661.023100
2.56-3.2326.60.0451112610.0090.0461.137100
3.23-5021.30.0311168410.0070.0321.22699.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RCN

3rcn


Resolution: 1.498→36.312 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 10.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1412 5422 4.96 %
Rwork0.1125 103826 -
obs0.1139 109248 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.59 Å2 / Biso mean: 22.6135 Å2 / Biso min: 9.8 Å2
Refinement stepCycle: final / Resolution: 1.498→36.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 5 753 4534
Biso mean--15.19 40.37 -
Num. residues----469
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4984-1.51550.22611710.15353310348198
1.5155-1.53330.17661890.143233773566100
1.5333-1.5520.16261680.130634273595100
1.552-1.57160.16481900.125134013591100
1.5716-1.59230.17091990.116933733572100
1.5923-1.61410.14291730.109434153588100
1.6141-1.63720.16851760.104634143590100
1.6372-1.66160.13981750.101634353610100
1.6616-1.68760.15221610.100634343595100
1.6876-1.71530.13771760.096634063582100
1.7153-1.74480.14161850.092833983583100
1.7448-1.77660.14481790.092634303609100
1.7766-1.81070.12711900.090634053595100
1.8107-1.84770.12681730.098934373610100
1.8477-1.88790.1421690.134413610100
1.8879-1.93180.14471810.105634503631100
1.9318-1.98010.13041990.102934273626100
1.9801-2.03360.14111740.097934443618100
2.0336-2.09340.13042010.097234073608100
2.0934-2.1610.13242030.100634283631100
2.161-2.23820.13662100.103734363646100
2.2382-2.32780.13891700.100734913661100
2.3278-2.43380.14271900.110534563646100
2.4338-2.5620.14181950.114534683663100
2.562-2.72250.15771630.118535163679100
2.7225-2.93260.14971590.126135543713100
2.9326-3.22760.14111850.122735383723100
3.2276-3.69420.13811710.105735753746100
3.6942-4.65280.11241650.101536573822100
4.6528-36.32260.15571820.150538764058100

+
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