[English] 日本語
Yorodumi
- PDB-6ve1: Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ve1
TitleCrystal structure of endo-beta-N-acetylglucosaminidase H at high pH
ComponentsEndo-beta-N-acetylglucosaminidase H
KeywordsHYDROLASE / SUGAR BINDING PROTEIN / enzyme / deglycosylase / post-translational modification
Function / homology
Function and homology information


mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase / mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Endo-beta-N-acetylglucosaminidase / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Endo-beta-N-acetylglucosaminidase H
Similarity search - Component
Biological speciesStreptomyces plicatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStachowski, T.R. / Snell, M.E. / Snell, E.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: Plos One / Year: 2020
Title: SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique.
Authors: Stachowski, T.R. / Snell, M.E. / Snell, E.H.
History
DepositionDec 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Endo-beta-N-acetylglucosaminidase H
B: Endo-beta-N-acetylglucosaminidase H
C: Endo-beta-N-acetylglucosaminidase H
D: Endo-beta-N-acetylglucosaminidase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,72010
Polymers121,5744
Non-polymers1466
Water20,4651136
1
A: Endo-beta-N-acetylglucosaminidase H
D: Endo-beta-N-acetylglucosaminidase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8605
Polymers60,7872
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-beta-N-acetylglucosaminidase H
C: Endo-beta-N-acetylglucosaminidase H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8605
Polymers60,7872
Non-polymers733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.480, 99.480, 135.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein
Endo-beta-N-acetylglucosaminidase H / DI-N-acetylchitobiosyl beta-N-acetylglucosaminidase H / Endoglycosidase H / Endo H / Mannosyl- ...DI-N-acetylchitobiosyl beta-N-acetylglucosaminidase H / Endoglycosidase H / Endo H / Mannosyl-glycoprotein endo-beta-N-acetyl-glucosaminidase H


Mass: 30393.506 Da / Num. of mol.: 4 / Fragment: UNP residues 47-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces plicatus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P04067, mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1136 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 9 / Details: PEG20000, magnesium nitrate, TAPS, pH 9.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41.031 Å / Num. obs: 74108 / % possible obs: 99.69 % / Redundancy: 2 % / CC1/2: 0.986 / Net I/σ(I): 5.89
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 7330 / CC1/2: 0.618

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EDT

1edt


Resolution: 2.1→41.031 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 31.22
RfactorNum. reflection% reflection
Rfree0.258 3647 4.93 %
Rwork0.2205 --
obs0.2225 73963 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.5 Å2 / Biso mean: 16.786 Å2 / Biso min: 1.82 Å2
Refinement stepCycle: final / Resolution: 2.1→41.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8111 0 6 1136 9253
Biso mean--26.43 24.78 -
Num. residues----1069
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.12760.38281600.34512670100
2.1276-2.15680.31411250.3112659100
2.1568-2.18760.32331310.29012703100
2.1876-2.22020.32781550.25972657100
2.2202-2.25490.31421280.26472668100
2.2549-2.29190.29911460.26082678100
2.2919-2.33140.32521530.24872665100
2.3314-2.37380.27271490.23742674100
2.3738-2.41950.26621400.23532688100
2.4195-2.46880.30651510.23542673100
2.4688-2.52250.27021400.22592676100
2.5225-2.58120.28441370.22222691100
2.5812-2.64570.27311290.21532694100
2.6457-2.71720.27241250.21762697100
2.7172-2.79720.2941470.22922690100
2.7972-2.88740.29231250.20542727100
2.8874-2.99060.23441390.20982700100
2.9906-3.11030.27811320.20532722100
3.1103-3.25180.20911320.20232688100
3.2518-3.42320.23291250.19762736100
3.4232-3.63750.23531410.18812703100
3.6375-3.91820.20651320.18342749100
3.9182-4.31210.22331450.1695272599
4.3121-4.93520.17271690.1696272199
4.9352-6.21430.24641500.21682795100
6.2143-41.0310.24781410.2528286798

+
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://pdbjlvh1.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