[English] 日本語
Yorodumi
- PDB-1scr: HIGH-RESOLUTION STRUCTURES OF SINGLE-METAL-SUBSTITUTED CONCANAVAL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1scr
TitleHIGH-RESOLUTION STRUCTURES OF SINGLE-METAL-SUBSTITUTED CONCANAVALIN A: THE CO,CA-PROTEIN AT 1.6 ANGSTROMS AND THE NI,CA-PROTEIN AT 2.0 ANGSTROMS
ComponentsCONCANAVALIN A
KeywordsLECTIN(AGGLUTININ)
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / metal ion binding
Similarity search - Function
Legume lectin / 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 ...Legume lectin / 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
NICKEL (II) ION / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsEmmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb, A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: High-resolution structures of single-metal-substituted concanavalin A: the Co,Ca-protein at 1.6 A and the Ni,Ca-protein at 2.0 A.
Authors: Emmerich, C. / Helliwell, J.R. / Redshaw, M. / Naismith, J.H. / Harrop, S.J. / Raftery, J. / Kalb, A.J. / Yariv, J. / Dauter, Z. / Wilson, K.S.
#1: Journal: Embo J. / Year: 1992
Title: Non-Glycosylated Recombinant Pro-Concanavalin a is Active without Polypeptide Cleavage
Authors: Min, W. / Dunn, A.J. / Jones
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: The Refined Structure of Cadmium Substituted Concanavalin a at 2.0 Angstroms Resolution
Authors: Naismith, J.H. / Habash, J. / Harrop, S.J. / Helliwell, J.R. / Hunter, W.N. / Wan, T.C.M. / Weisgerber, S. / Kalb(Gilboa), A.J. / Yariv, J.
#3: Journal: J.Cryst.Growth / Year: 1988
Title: The Effect of Metal Ion Homogeneity on the Diffraction Limit of Orthorhombic I222 Crystals of Concanavalin A
Authors: Kalb(Gilboa), A.J. / Yariv, J. / Helliwell, J.R. / Papiz, M.Z.
History
DepositionDec 6, 1993Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7213
Polymers25,6221
Non-polymers992
Water2,594144
1
A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules

A: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,88512
Polymers102,4904
Non-polymers3958
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area10080 Å2
ΔGint-130 kcal/mol
Surface area33330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.440, 87.210, 63.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: ALA 207 - ASP 208 OMEGA = 0.43 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Components on special symmetry positions
IDModelComponents
11A-383-

HOH

DetailsTHERE IS ONE MONOMER (237 AMINO ACIDS) IN THE ASYMMETRIC UNIT. CONCANAVALIN A EXISTS AS A TETRAMER ALTHOUGH THE ASYMMETRIC UNIT CONTAINS A MONOMER. THE TETRAMER CAN BE GENERATED BY SYMMETRY OPERATORS.

-
Components

#1: Protein CONCANAVALIN A


Mass: 25622.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canavalia ensiformis (jack bean) / Gene: CDNA / Organ: BEAN / References: UniProt: P02866
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Compound detailsKALB ET AL. (1988) POSTULATED IN A SURVEY OF THE RESOLUTION LIMITS OF A VARIETY OF METAL ...KALB ET AL. (1988) POSTULATED IN A SURVEY OF THE RESOLUTION LIMITS OF A VARIETY OF METAL SUBSTITUTED CONCANAVALIN A'S THAT THERE WAS INCREASED DISORDER CAUSED BY SMALLER TRANSITION METAL IONS. EMMERICH ET AL. (1993) COMPARED THE CO,CA- AND NI,CA-CONCANAVALIN A STRUCTURES. THE NI,CA-CONCANAVALIN A COORDINATES ARE REPORTED HERE. IT IS FOUND THAT THERE IS SOME CORRELATION BETWEEN THE TRANSITION METAL ION AND THE DEGREES OF DISORDER IN THE ENTIRE MOLECULE AND THUS THE RESOLUTION LIMIT OF THE CRYSTAL. HOWEVER, IT IS AN OVER-SIMPLIFICATION TO CORRELATE ONLY WITH IONIC RADIUS.
Sequence detailsTHE SEQUENCE IS AS DERIVED FROM THE CDNA SEQUENCE OF MIN ET AL.,1992.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal grow
*PLUS
pH: 6.5 / Method: microdialysis / Details: Greer, J., (1970) J. Mol. Biol, 48, 365.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 M11NaNO3
20.05 MTris acetate11

-
Data collection

Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 16435 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Num. measured all: 60304 / Rmerge(I) obs: 0.04

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.159 -
obs0.159 16128
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 2 144 1955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.159 / Rfactor Rwork: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.8

+
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