[English] 日本語
Yorodumi
- PDB-4wka: Crystal structure of human chitotriosidase-1 catalytic domain at ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wka
TitleCrystal structure of human chitotriosidase-1 catalytic domain at 0.95 A resolution
ComponentsChitotriosidase-1
KeywordsHYDROLASE / CHIT1 / GH18 chitinase / protonation states / hydrolysis / catalytic mechanism
Function / homology
Function and homology information


polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium / specific granule lumen / tertiary granule lumen / lysosome / immune response / Neutrophil degranulation / extracellular space / 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 / Chitinase A; domain 3 - #10 / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / : / Chitinase insertion domain superfamily ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Chitinase A; domain 3 - #10 / 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. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Chitinase A; domain 3 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Roll / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Chitotriosidase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsFadel, F. / Zhao, Y. / Cachau, R. / Cousido-Siah, A. / Ruiz, F.X. / Harlos, K. / Howard, E. / Mitschler, A. / Podjarny, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM.
Authors: Fadel, F. / Zhao, Y. / Cachau, R. / Cousido-Siah, A. / Ruiz, F.X. / Harlos, K. / Howard, E. / Mitschler, A. / Podjarny, A.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5243
Polymers42,2241
Non-polymers3002
Water10,215567
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint1 kcal/mol
Surface area15210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.327, 103.701, 41.688
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Chitotriosidase-1 / Chitinase-1


Mass: 42224.289 Da / Num. of mol.: 1 / Fragment: UNP residues 22-386
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHIT1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q13231, chitinase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 23 % (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate (PST) at pH 7.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2014
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.95→50 Å / Num. obs: 223038 / % possible obs: 95.99 % / Redundancy: 12.6 % / Rsym value: 0.059 / Net I/σ(I): 36.08
Reflection shellResolution: 0.95→0.98 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2.57 / % possible all: 82.51

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1702)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GUV

1guv


Resolution: 0.95→42.663 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 9.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1227 11188 5.02 %Random 5%
Rwork0.1123 ---
obs0.1129 223022 95.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.95→42.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 20 567 3496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073591
X-RAY DIFFRACTIONf_angle_d1.3234926
X-RAY DIFFRACTIONf_dihedral_angle_d14.6331343
X-RAY DIFFRACTIONf_chiral_restr0.081501
X-RAY DIFFRACTIONf_plane_restr0.007672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9502-0.9610.23332770.23965586X-RAY DIFFRACTION77
0.961-0.97230.20892850.20986075X-RAY DIFFRACTION83
0.9723-0.98410.1883410.19276360X-RAY DIFFRACTION88
0.9841-0.99660.18033420.17576660X-RAY DIFFRACTION91
0.9966-1.00970.15973490.1596808X-RAY DIFFRACTION93
1.0097-1.02350.16033490.13986953X-RAY DIFFRACTION95
1.0235-1.03820.14143660.1226982X-RAY DIFFRACTION96
1.0382-1.05360.12363540.11137056X-RAY DIFFRACTION97
1.0536-1.07010.11733490.10547033X-RAY DIFFRACTION96
1.0701-1.08770.11893710.09727086X-RAY DIFFRACTION97
1.0877-1.10640.10474220.09257038X-RAY DIFFRACTION97
1.1064-1.12650.11063770.09137129X-RAY DIFFRACTION97
1.1265-1.14820.10123470.08887080X-RAY DIFFRACTION97
1.1482-1.17160.10083990.08517110X-RAY DIFFRACTION97
1.1716-1.19710.09643630.08637145X-RAY DIFFRACTION98
1.1971-1.2250.09744110.08527102X-RAY DIFFRACTION97
1.225-1.25560.1073880.08637198X-RAY DIFFRACTION98
1.2556-1.28960.10783540.0887191X-RAY DIFFRACTION98
1.2896-1.32750.1023960.08767220X-RAY DIFFRACTION98
1.3275-1.37040.10294160.08887185X-RAY DIFFRACTION98
1.3704-1.41930.10793710.08987278X-RAY DIFFRACTION99
1.4193-1.47620.09723810.09357261X-RAY DIFFRACTION99
1.4762-1.54340.11824080.09287259X-RAY DIFFRACTION98
1.5434-1.62470.10593890.09577281X-RAY DIFFRACTION99
1.6247-1.72650.124020.10127367X-RAY DIFFRACTION99
1.7265-1.85980.11713920.10727358X-RAY DIFFRACTION99
1.8598-2.0470.11633650.11017422X-RAY DIFFRACTION100
2.047-2.34320.12214100.11137461X-RAY DIFFRACTION100
2.3432-2.95210.13334010.12777537X-RAY DIFFRACTION100
2.9521-42.70660.13914130.13557613X-RAY DIFFRACTION97

+
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