[English] 日本語
Yorodumi
- PDB-6k7z: Crystal structure of a GH18 chitinase from Pseudoalteromonas aurantia -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6k7z
TitleCrystal structure of a GH18 chitinase from Pseudoalteromonas aurantia
ComponentsGH18 chiitnase
KeywordsHYDROLASE / Chitinase / GH18 / Carbohydrate
Function / homology
Function and homology information


chitinase activity / chitinase / chitin binding / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesPseudoalteromonas aurantia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsWang, Y.J. / Li, P.Y. / Cao, H.Y. / Chen, X.L. / Zhang, Y.Z.
Funding support China, 3items
OrganizationGrant numberCountry
National Science Foundation (China)91851205 China
National Science Foundation (China)41676180 China
National Science Foundation (China)91751101 China
CitationJournal: Front Microbiol / Year: 2019
Title: Structural Insight Into Chitin Degradation and Thermostability of a Novel Endochitinase From the Glycoside Hydrolase Family 18.
Authors: Wang, Y.J. / Jiang, W.X. / Zhang, Y.S. / Cao, H.Y. / Zhang, Y. / Chen, X.L. / Li, C.Y. / Wang, P. / Zhang, Y.Z. / Song, X.Y. / Li, P.Y.
History
DepositionJun 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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: GH18 chiitnase
B: GH18 chiitnase
C: GH18 chiitnase
D: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)126,2364
Polymers126,2364
Non-polymers00
Water17,853991
1
A: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)31,5591
Polymers31,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)31,5591
Polymers31,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)31,5591
Polymers31,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GH18 chiitnase


Theoretical massNumber of molelcules
Total (without water)31,5591
Polymers31,5591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.618, 87.486, 88.836
Angle α, β, γ (deg.)90.00, 95.30, 90.00
Int Tables number3
Space group name H-MP121

-
Components

#1: Protein
GH18 chiitnase


Mass: 31559.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas aurantia (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A650AJ72*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 991 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 8000, 0.05 M KH2PO4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 96262 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 30.3
Reflection shellResolution: 1.799→1.863 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 10.2 / Num. unique obs: 9086

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSJ

2gsj


Resolution: 1.799→33.019 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 46.81
RfactorNum. reflection% reflection
Rfree0.2372 4511 4.72 %
Rwork0.2121 --
obs0.2133 95543 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.799→33.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8448 0 0 991 9439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068704
X-RAY DIFFRACTIONf_angle_d0.84311872
X-RAY DIFFRACTIONf_dihedral_angle_d11.5585168
X-RAY DIFFRACTIONf_chiral_restr0.0531320
X-RAY DIFFRACTIONf_plane_restr0.0061560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7992-1.81960.30791270.26052535X-RAY DIFFRACTION82
1.8196-1.8410.32221450.26223008X-RAY DIFFRACTION100
1.841-1.86350.29631350.25263120X-RAY DIFFRACTION100
1.8635-1.8870.26491370.25733078X-RAY DIFFRACTION100
1.887-1.91190.23341020.24923095X-RAY DIFFRACTION100
1.9119-1.93810.26161350.24983055X-RAY DIFFRACTION100
1.9381-1.96570.24911590.23543011X-RAY DIFFRACTION99
1.9657-1.99510.24481520.23693068X-RAY DIFFRACTION100
1.9951-2.02620.24551480.23163091X-RAY DIFFRACTION100
2.0262-2.05950.21791540.23873069X-RAY DIFFRACTION100
2.0595-2.0950.24971590.2283039X-RAY DIFFRACTION100
2.095-2.13310.21861440.22373050X-RAY DIFFRACTION99
2.1331-2.17410.2671490.22583042X-RAY DIFFRACTION100
2.1741-2.21840.22521560.22253097X-RAY DIFFRACTION100
2.2184-2.26670.24951450.22273058X-RAY DIFFRACTION100
2.2667-2.31940.22061550.21893027X-RAY DIFFRACTION99
2.3194-2.37740.20531410.22473068X-RAY DIFFRACTION99
2.3774-2.44160.28891480.22083080X-RAY DIFFRACTION100
2.4416-2.51350.26621630.21813022X-RAY DIFFRACTION99
2.5135-2.59460.26921700.20213031X-RAY DIFFRACTION99
2.5946-2.68720.24831520.20583066X-RAY DIFFRACTION100
2.6872-2.79480.23981690.20513042X-RAY DIFFRACTION100
2.7948-2.92190.23181880.21453028X-RAY DIFFRACTION99
2.9219-3.07590.1841780.20593034X-RAY DIFFRACTION99
3.0759-3.26840.23021670.20573049X-RAY DIFFRACTION99
3.2684-3.52050.21741590.20463020X-RAY DIFFRACTION99
3.5205-3.87430.23081370.20243078X-RAY DIFFRACTION98
3.8743-4.43380.23181420.17823083X-RAY DIFFRACTION99
4.4338-5.58170.22361670.17833077X-RAY DIFFRACTION99
5.5817-33.02430.23511280.19362911X-RAY DIFFRACTION91

+
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