[English] 日本語
Yorodumi
- PDB-1bf0: CALCICLUDINE (CAC) FROM GREEN MAMBA DENDROASPIS ANGUSTICEPS, NMR,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bf0
TitleCALCICLUDINE (CAC) FROM GREEN MAMBA DENDROASPIS ANGUSTICEPS, NMR, 15 STRUCTURES
ComponentsCALCICLUDINE
KeywordsCALCIUM CHANNEL BLOCKER
Function / homology
Function and homology information


calcium channel regulator activity / serine-type endopeptidase inhibitor activity / toxin activity / extracellular space
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Kunitz-type serine protease inhibitor homolog calcicludine
Similarity search - Component
Biological speciesDendroaspis angusticeps (eastern green mamba)
MethodSOLUTION NMR / MD- BASED SIMULATED ANNEALING WITH AMBIGOUS DISTANCE CONSTRAINTS
AuthorsGilquin, B. / Lecoq, A. / Desne, F. / Guenneugues, M. / Zinn-Justin, S. / Menez, A.
CitationJournal: Proteins / Year: 1999
Title: Conformational and functional variability supported by the BPTI fold: solution structure of the Ca2+ channel blocker calcicludine.
Authors: Gilquin, B. / Lecoq, A. / Desne, F. / Guenneugues, M. / Zinn-Justin, S. / Menez, A.
History
DepositionMay 26, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_src_gen / entity_src_nat / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.src_method / _pdbx_database_status.process_site / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.version / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CALCICLUDINE


Theoretical massNumber of molelcules
Total (without water)6,9981
Polymers6,9981
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100LEAST RESTRAINT VIOLATION
RepresentativeModel #1

-
Components

#1: Protein CALCICLUDINE /


Mass: 6998.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: venom
Source: (natural) Dendroaspis angusticeps (eastern green mamba)
References: UniProt: P81658

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121COSY
131TOCSY
NMR detailsText: COLLECTION OF ANGLE AND DISTANCE CONSTRAINTS WERE DERIVED FROM DQF-COSY AND NOESY EXPERIMENT RESPECTIVELY, CARRIED OUT IN H2O AND D2O. MIXING TIME OF 50, 75, 100 AND 150 MS WERE USED IN THE ...Text: COLLECTION OF ANGLE AND DISTANCE CONSTRAINTS WERE DERIVED FROM DQF-COSY AND NOESY EXPERIMENT RESPECTIVELY, CARRIED OUT IN H2O AND D2O. MIXING TIME OF 50, 75, 100 AND 150 MS WERE USED IN THE NOESY EXPERIMENTS. DISTANCE CONSTRAINTS WERE DERIVED FROM THE BUILD-UP CURVES RATES BY APPLYING AN AUTOMATED ITERATIVE ASSIGNMENT PROCEDURE.

-
Sample preparation

Sample conditionspH: 4.5 / Temperature: 30 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure calculation
RefinementMethod: MD- BASED SIMULATED ANNEALING WITH AMBIGOUS DISTANCE CONSTRAINTS
Software ordinal: 1
Details: DETAILS ON THE STRUCTURE CALCULATION CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 100 / Conformers submitted total number: 15

+
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