[English] 日本語
Yorodumi
- PDB-6g9e: Crystal structure of immunomodulatory active chitinase from Trich... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6g9e
TitleCrystal structure of immunomodulatory active chitinase from Trichuris suis - TsES1 - 6 molecules in ASU
ComponentsImmunomodulatory active chitinase
KeywordsHYDROLASE / TsES1 / immunomodulatory potential / chitinase / Eukaryotic protein expression / LEXSY / secretion / dimer / intramolecular disulphide bridge
Function / homology
Function and homology information


chitinase activity / chitin catabolic process / chitin binding / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chitin-binding type-2 domain-containing protein
Similarity search - Component
Biological speciesTrichuris suis (pig whipworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsMalecki, P.H. / Balster, K. / Hartmann, S. / Weiss, M.S. / Heinemann, U.
CitationJournal: J Immunol Res / Year: 2021
Title: A Helminth-Derived Chitinase Structurally Similar to Mammalian Chitinase Displays Immunomodulatory Properties in Inflammatory Lung Disease.
Authors: Ebner, F. / Lindner, K. / Janek, K. / Niewienda, A. / Malecki, P.H. / Weiss, M.S. / Sutherland, T.E. / Heuser, A. / Kuhl, A.A. / Zentek, J. / Hofmann, A. / Hartmann, S.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunomodulatory active chitinase
B: Immunomodulatory active chitinase
C: Immunomodulatory active chitinase
D: Immunomodulatory active chitinase
E: Immunomodulatory active chitinase
F: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,58411
Polymers333,2746
Non-polymers3105
Water8,161453
1
A: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6082
Polymers55,5461
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6082
Polymers55,5461
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6703
Polymers55,5461
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Immunomodulatory active chitinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6082
Polymers55,5461
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Immunomodulatory active chitinase


Theoretical massNumber of molelcules
Total (without water)55,5461
Polymers55,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Immunomodulatory active chitinase


Theoretical massNumber of molelcules
Total (without water)55,5461
Polymers55,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.063, 172.618, 138.564
Angle α, β, γ (deg.)90.000, 128.410, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-684-

HOH

-
Components

#1: Protein
Immunomodulatory active chitinase


Mass: 55545.691 Da / Num. of mol.: 6 / Fragment: TsES1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichuris suis (pig whipworm) / Gene: M513_10624 / Production host: Leishmania tarentolae (eukaryote) / References: UniProt: A0A085LU44
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 4.09 Å3/Da / Density % sol: 69.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 100mM Tris, 200mM Magnesium chloride hexahydrate, 10% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2017
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.69→45.61 Å / Num. obs: 110673 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 37.83 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.267 / Rpim(I) all: 0.155 / Rrim(I) all: 0.31 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.69-2.743.71.30349520.4880.7671.51789.5
14.75-45.613.40.0666860.9910.0410.07995.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.6.2data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hbf

5hbf


Resolution: 2.69→45.61 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.44
RfactorNum. reflection% reflection
Rfree0.2491 1103 1 %
Rwork0.1925 --
obs0.193 110597 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.97 Å2 / Biso mean: 43.0582 Å2 / Biso min: 16.8 Å2
Refinement stepCycle: final / Resolution: 2.69→45.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17772 0 20 455 18247
Biso mean--54.99 35.4 -
Num. residues----2208
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.69-2.81560.37181460.30331313995
2.8156-2.9640.32161430.26351369399
2.964-3.14960.27171490.252513717100
3.1496-3.39280.2881930.22881367799
3.3928-3.7340.25141040.18671374199
3.734-4.2740.21141380.157513819100
4.274-5.38340.1803950.14121382599
5.3834-45.610.20471350.16981388399
Refinement TLS params.Method: refined / Origin x: 12.3924 Å / Origin y: 5.3288 Å / Origin z: 130.6447 Å
111213212223313233
T0.228 Å20.011 Å20.0427 Å2-0.2429 Å20.0009 Å2--0.2258 Å2
L0.5704 °20.0419 °20.0179 °2-0.3468 °2-0.0174 °2--0.2552 °2
S0.0099 Å °-0.1475 Å °0.0174 Å °0.1066 Å °-0.0045 Å °-0.0304 Å °-0.0105 Å °0.0152 Å °-0.0055 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA32 - 399
2X-RAY DIFFRACTION1allB32 - 399
3X-RAY DIFFRACTION1allC32 - 399
4X-RAY DIFFRACTION1allD32 - 399
5X-RAY DIFFRACTION1allE32 - 399
6X-RAY DIFFRACTION1allF32 - 399
7X-RAY DIFFRACTION1allG1 - 474
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allH2
10X-RAY DIFFRACTION1allH3 - 5
11X-RAY DIFFRACTION1allH6

+
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