[English] 日本語
Yorodumi
- PDB-2lhs: Structure of the chitin binding protein 21 (CBP21) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lhs
TitleStructure of the chitin binding protein 21 (CBP21)
ComponentsCBP21
KeywordsChitin Binding Protein
Function / homologychitin-binding protein cbp21 / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Coagulation Factor XIII; Chain A, domain 1 / chitin catabolic process / Distorted Sandwich / Immunoglobulin E-set / Mainly Beta / CBP21
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 20
AuthorsAachmann, F.L. / Eijsink, V.G. / Vaaje-Kolstad, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: NMR structure of a lytic polysaccharide monooxygenase provides insight into copper binding, protein dynamics, and substrate interactions.
Authors: Aachmann, F.L. / Sorlie, M. / Skjak-Braek, G. / Eijsink, V.G. / Vaaje-Kolstad, G.
History
DepositionAug 15, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Aug 13, 2014Group: Database references
Revision 1.4Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR
Remark 700 SHEET DETERMINATION METHOD: AUTHOR

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CBP21


Theoretical massNumber of molelcules
Total (without water)18,8131
Polymers18,8131
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein CBP21 / Chitin-binding protein


Mass: 18812.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: BJL200 / Gene: cbp / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83009

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 1H-13C NOESY aliphatic
1213D 1H-15N NOESY
1332D 1H-1H TOCSY
1432D DQF-COSY
1532D 1H-1H NOESY
1622D 1H-13C HSQC aromatic
1742D DQF-COSY
1842D 1H-1H TOCSY
1942D 1H-1H NOESY
11012D 1H-13C HSQC aliphatic

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.8-1.2 mM [U-98% 13C; U-98% 15N] CBP21, 20 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
20.8-1.2 mM [U-98% 13C; U-98% 15N] CBP21, 20 mM potassium phosphate, 10 mM sodium chloride, 100% D2O100% D2O
30.8-1.2 mM CBP21, 20 mM potassium phosphate, 10 mM sodium chloride, 90% H2O/10% D2O90% H2O/10% D2O
40.8-1.2 mM CBP21, 20 mM potassium phosphate, 10 mM sodium chloride, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMCBP21-1[U-98% 13C; U-98% 15N]0.8-1.21
20 mMpotassium phosphate-21
10 mMsodium chloride-31
mMCBP21-4[U-98% 13C; U-98% 15N]0.8-1.22
20 mMpotassium phosphate-52
10 mMsodium chloride-62
mMCBP21-70.8-1.23
20 mMpotassium phosphate-83
10 mMsodium chloride-93
mMCBP21-100.8-1.24
20 mMpotassium phosphate-114
10 mMsodium chloride-124
Sample conditionsIonic strength: 0.06 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XEASYBartels et al.collection
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
YASARAKrieger, Darden, Nabuurs, Finkelstein, Vriendrefinement
CYANAKrieger, Darden, Nabuurs, Finkelstein, Vriendrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 256 / Conformers submitted total number: 20

+
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