[English] 日本語
Yorodumi
- PDB-1dq0: Locked, metal-free concanavalin A, a minor species in solution -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dq0
TitleLocked, metal-free concanavalin A, a minor species in solution
ComponentsConcanavalin-Br
KeywordsSUGAR BINDING PROTEIN / MINOR STRUCTURAL SPECIES / SOLUTION / LOCKED STATE / DEMETALLIZED CONCANAVALIN A / BETA-SHEET
Function / homology
Function and homology information


D-mannose binding / toxin activity / metal ion binding
Similarity search - Function
Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBouckaert, J. / Dewallef, Y. / Poortmans, F. / Wyns, L. / Loris, R.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The structural features of concanavalin A governing non-proline peptide isomerization
Authors: Bouckaert, J. / Dewallef, Y. / Poortmans, F. / Wyns, L. / Loris, R.
History
DepositionDec 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Aug 9, 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: Concanavalin-Br


Theoretical massNumber of molelcules
Total (without water)25,6221
Polymers25,6221
Non-polymers00
Water3,315184
1
A: Concanavalin-Br

A: Concanavalin-Br

A: Concanavalin-Br

A: Concanavalin-Br


Theoretical massNumber of molelcules
Total (without water)102,4904
Polymers102,4904
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_546x,-y-1,-z+11
Unit cell
Length a, b, c (Å)63.006, 87.290, 88.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-484-

HOH

-
Components

#1: Protein Concanavalin-Br / Con Br / LOCKED METAL-FREE CONCANAVALIN A


Mass: 25622.385 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P55915
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 293 K / pH: 7
Details: 2.1 M AMMONIUM SULPHATE, 120 MM SODIUM ACETATE, SOAKING OF LOCKED MNMN CON A CRYSTALS WITH THE METAL CHELATOR EDTA, pH 7.0, temperature 293.0K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117.3 mg/mlmetal-free ConA1drop
22 Mammonium sulfate1drop
360 mM1dropCH3COONa
43 %mPEG50001drop
58 mM1reservoirMnCl2
62 Mammonium sulfate1reservoir
760 mM1reservoirCH3COONa
83 %mPEG50001reservoir

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 24, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→26 Å / Num. all: 312000 / Num. obs: 311946 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 15 Å2 / Rfree details: 10 / Rmerge(I) obs: 0.061 / Net I/σ(I): 22.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 5.7 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 27215 / Num. measured all: 311946
Reflection shell
*PLUS
% possible obs: 99.9 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementStarting model: 1CON

1con


Resolution: 1.7→26 Å / Cross valid method: BRUNGER / σ(F): 0 / σ(I): -3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2721 10 %RANDOM
Rwork0.181 ---
all0.181 27215 --
obs0.181 27215 99.7 %-
Refinement stepCycle: LAST / Resolution: 1.7→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 0 185 2005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_dihedral_angle_d27.1
X-RAY DIFFRACTIONx_improper_angle_d1.7
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.312 / Rfactor Rwork: 0.301

+
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