[English] 日本語
Yorodumi
- PDB-1cxr: AUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cxr
TitleAUTOMATED 2D NOESY ASSIGNMENT AND STRUCTURE CALCULATION OF CRAMBIN(S22/I25) WITH SELF-CORRECTING DISTANCE GEOMETRY BASED NOAH/DIAMOD PROGRAMS
ComponentsCRAMBIN
KeywordsPLANT PROTEIN / CRAMBIN / CRAMBE ABYSSINICA / PLANT SEED PROTEIN FEB. 20 / 1997
Function / homology
Function and homology information


defense response / extracellular region
Similarity search - Function
Thionin-like / Thionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / Crambin / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCrambe hispanica subsp. abyssinica (Abyssinian crambe)
MethodSOLUTION NMR / SELF-CORRECTING DISTANCE GEOMETRY
AuthorsXu, Y. / Wu, J. / Gorenstein, D. / Braun, W.
Citation
Journal: J.Magn.Reson. / Year: 1999
Title: Automated 2D NOESY assignment and structure calculation of Crambin(S22/I25) with the self-correcting distance geometry based NOAH/DIAMOD programs.
Authors: Xu, Y. / Wu, J. / Gorenstein, D. / Braun, W.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Automated Assignment of Simulated, Experimental Noesy Spectra of Proteins by Feedback Filtering and Self-Correcting Distance Geometry
Authors: Mumenthaler, C. / Braun, W.
#2: Journal: J.Biomol.NMR / Year: 1997
Title: Automated Combined Assignment of Noesy Spectra and Three-Dimensional Protein Structure Determination
Authors: Mumenthaler, C. / Guntert, P. / Braun, W. / Wuthrich, K.
#3: Journal: Biological Magnetic Resonance / Year: 1999
Title: Combined Automated Assignment of NMR Spectra and Calculation of Three- Dimensional Protein Structures
Authors: Xu, Y. / Schein, C.H. / Braun, W.
#4: Journal: Biopolymers / Year: 1990
Title: A Program, Fantom, for Energy Refinement of Polypeptides and Proteins Using a Newton-Raphson Minimizer in the Torsion Angle Space
Authors: Schaumann, T.H. / Braun, W. / Wuthrich, K.
#5: Journal: J.Comput.Chem. / Year: 1998
Title: Exact and Efficient Analytical Calculation of the Accessible Surface Areas and Their Gradients Macromolecules
Authors: Fraczkiewicz, R. / Braun, W.
History
DepositionAug 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation_author.name
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRAMBIN


Theoretical massNumber of molelcules
Total (without water)4,7281
Polymers4,7281
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION
RepresentativeModel #8closest to the average

-
Components

#1: Protein/peptide CRAMBIN /


Mass: 4728.410 Da / Num. of mol.: 1 / Fragment: ISOFORM OF CRAMBIN (46 RESIDUES) / Mutation: S22P, I25L / Source method: isolated from a natural source
Source: (natural) Crambe hispanica subsp. abyssinica (Abyssinian crambe)
Organ: SEED / Species: Crambe hispanica / Strain: subsp. abyssinica / References: UniProt: P01542

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
222DQF-COSY
3332D TOCSY
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES.

-
Sample preparation

DetailsContents: 2.5 MM CRAMBIN(SER/ILE) 0.7 ML OF 75% D6-ACETONE, 20%H2O,5%D2O BUFFER
Sample conditionspH: 6.5 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian VXRS / Manufacturer: Varian / Model: VXRS / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
NOAH1C.MUMENTHALER, Y.XU, W.BRAUNstructure solution
DIAMOD1P. GUNTERT, W. BRAUN, K. WUTHRICHstructure solution
FANTOM4TH.SCHAUMANN, W.BRAUN, K.WUTHRICH, R.FRACZKIEWICZrefinement
RefinementMethod: SELF-CORRECTING DISTANCE GEOMETRY / Software ordinal: 1 / Details: SEE REFERENCE: J. MAGN. RESON. 136, P76-85(1999)
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY,TARGET FUNCTION
Conformers calculated total number: 40 / Conformers submitted total number: 10

+
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