[English] 日本語
Yorodumi
- PDB-2cau: CANAVALIN FROM JACK BEAN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cau
TitleCANAVALIN FROM JACK BEAN
ComponentsPROTEIN (CANAVALIN)
KeywordsPLANT PROTEIN / VICILIN / 7S SEED PROTEIN / DOMAIN DUPLICATION / SWISS ROLL
Function / homology
Function and homology information


nutrient reservoir activity / protein-containing complex / identical protein binding
Similarity search - Function
Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKo, T.-P. / Day, J. / Macpherson, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The refined structure of canavalin from jack bean in two crystal forms at 2.1 and 2.0 A resolution.
Authors: Ko, T.P. / Day, J. / McPherson, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Determination of Three Crystal Structures of Canavalin by Molecular Replacement
Authors: Ko, T.-P. / Ng, J.D. / Day, J. / Greenwood, A. / Macpherson, A.
History
DepositionNov 20, 1998Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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: PROTEIN (CANAVALIN)


Theoretical massNumber of molelcules
Total (without water)50,3831
Polymers50,3831
Non-polymers00
Water1,820101
1
A: PROTEIN (CANAVALIN)

A: PROTEIN (CANAVALIN)

A: PROTEIN (CANAVALIN)


Theoretical massNumber of molelcules
Total (without water)151,1503
Polymers151,1503
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area14330 Å2
ΔGint-97 kcal/mol
Surface area36830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.990, 105.990, 105.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

21A-502-

HOH

31A-503-

HOH

-
Components

#1: Protein PROTEIN (CANAVALIN) / JACK BEAN VICILIN


Mass: 50383.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TREATED WITH LIMITED DIGESTION BY TRYPSIN / Source: (natural) Canavalia ensiformis (jack bean) / Cellular location: PROTEIN BODY / Organ: SEED / Tissue: COTYLEDON / Keywords: TREATED WITH LIMITED DIGESTION BY TRYPSIN / References: UniProt: P50477
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.3 Å3/Da / Density % sol: 46 % / Description: REFERENCE TO PDB1CAU
Crystal growpH: 6.8
Details: THIS CRYSTAL FORM COULD BE GROWN ONLY OCCASIONALLY. BASICALLY IT WAS CRYSTALLIZED FROM PURIFIED PROTEIN AFTER TRYPSIN TREATMENT IN PHOSPHATE BUFFERED SALINE, BUT WAS DIFFICULT TO REPRODUCE., pH 6.8
Crystal grow
*PLUS
Temperature: 277-281 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein1drop
21.0 %1dropNaCl
350 mMphosphate1drop

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→40 Å / Num. obs: 22331 / % possible obs: 85.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 21
Reflection shellResolution: 2.02→2.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 3 / % possible all: 66.5
Reflection
*PLUS
Num. measured all: 71863
Reflection shell
*PLUS
% possible obs: 66.5 % / Num. unique obs: 3415 / Num. measured obs: 5944

-
Processing

Software
NameVersionClassification
MERLOTphasing
X-PLOR3.8refinement
SDMSdata reduction
SDMSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CAV

1cav


Resolution: 2.1→40 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1523 8 %RANDOM
Rwork0.175 ---
obs-19695 84 %-
Displacement parametersBiso mean: 28.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-40 Å
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 0 101 2865
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.569
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.729
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.521.5
X-RAY DIFFRACTIONx_mcangle_it2.522
X-RAY DIFFRACTIONx_scbond_it2.82
X-RAY DIFFRACTIONx_scangle_it4.512.5
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.291 180 6.2 %
Rwork0.239 1929 -
obs--72.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / σ(F): 2 / % reflection Rfree: 8 % / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.729
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.291 / % reflection Rfree: 6.2 % / Rfactor Rwork: 0.239 / Rfactor obs: 0.239

+
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