[English] 日本語
Yorodumi
- PDB-5z3c: Glycosidase E178A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5z3c
TitleGlycosidase E178A
ComponentsGlycoside hydrolase 15-related protein
KeywordsHYDROLASE / Glycosidase
Function / homologyisomaltose glucohydrolase / GH15-like domain / Glycosyl hydrolases family 15 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / cytoplasm / Isomaltose glucohydrolase
Function and homology information
Biological speciesKribbella flavida DSM 17836 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsTanaka, Y. / Chen, M. / Tagami, T. / Yao, M. / Kimura, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Platform for Drug Discovery, Informatics, and Structural Life Science(PDIS) Japan
CitationJournal: Febs J. / Year: 2022
Title: Structural insights reveal the second base catalyst of isomaltose glucohydrolase.
Authors: Tagami, T. / Chen, M. / Furunaga, Y. / Kikuchi, A. / Sadahiro, J. / Lang, W. / Okuyama, M. / Tanaka, Y. / Iwasaki, T. / Yao, M. / Kimura, A.
History
DepositionJan 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycoside hydrolase 15-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4306
Polymers43,9701
Non-polymers4605
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.917, 104.917, 89.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-576-

HOH

21A-595-

HOH

31A-704-

HOH

41A-766-

HOH

-
Components

#1: Protein Glycoside hydrolase 15-related protein


Mass: 43970.023 Da / Num. of mol.: 1 / Mutation: E178A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kribbella flavida DSM 17836 (bacteria) / Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_1896 / Production host: Escherichia coli (E. coli) / References: UniProt: D2PPM8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium citrate tribasic (pH 6.8), 0.1M Sodium citrate (pH 5.5), 12% PEGmonomethyl ether 2000, 2mM isomaltose

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→45.26 Å / Num. obs: 66196 / % possible obs: 99.9 % / Redundancy: 21.7 % / Net I/σ(I): 38.12
Reflection shellResolution: 1.6→1.69 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.6→45.257 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.91
RfactorNum. reflection% reflection
Rfree0.1571 3310 5 %
Rwork0.1338 --
obs0.135 66192 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→45.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 30 339 3227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133025
X-RAY DIFFRACTIONf_angle_d1.4254134
X-RAY DIFFRACTIONf_dihedral_angle_d12.561032
X-RAY DIFFRACTIONf_chiral_restr0.058432
X-RAY DIFFRACTIONf_plane_restr0.009537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6003-1.62310.22321340.16042540X-RAY DIFFRACTION98
1.6231-1.64740.18511370.14562581X-RAY DIFFRACTION100
1.6474-1.67310.16881350.14412576X-RAY DIFFRACTION100
1.6731-1.70050.16221380.1412592X-RAY DIFFRACTION100
1.7005-1.72990.15021330.13432575X-RAY DIFFRACTION100
1.7299-1.76130.15661360.1362589X-RAY DIFFRACTION100
1.7613-1.79520.17021370.13272588X-RAY DIFFRACTION100
1.7952-1.83180.16741380.13932602X-RAY DIFFRACTION100
1.8318-1.87170.17361360.13892586X-RAY DIFFRACTION100
1.8717-1.91520.19681360.14032601X-RAY DIFFRACTION100
1.9152-1.96310.14881360.14022577X-RAY DIFFRACTION100
1.9631-2.01620.17231380.12892609X-RAY DIFFRACTION100
2.0162-2.07550.16071360.13012593X-RAY DIFFRACTION100
2.0755-2.14250.131360.12762602X-RAY DIFFRACTION100
2.1425-2.21910.13861380.12182620X-RAY DIFFRACTION100
2.2191-2.30790.12651380.12092616X-RAY DIFFRACTION100
2.3079-2.4130.14631380.12032610X-RAY DIFFRACTION100
2.413-2.54020.17251380.12612623X-RAY DIFFRACTION100
2.5402-2.69930.13971400.12662664X-RAY DIFFRACTION100
2.6993-2.90770.17131380.1312627X-RAY DIFFRACTION100
2.9077-3.20020.15341390.13982653X-RAY DIFFRACTION100
3.2002-3.66310.17161420.14652675X-RAY DIFFRACTION100
3.6631-4.61440.13791420.12642716X-RAY DIFFRACTION100
4.6144-45.27530.16471510.14352867X-RAY DIFFRACTION100

+
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