[English] 日本語
Yorodumi
- PDB-1len: REFINEMENT OF TWO CRYSTAL FORMS OF LENTIL LECTIN AT 1.8 ANGSTROMS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1len
TitleREFINEMENT OF TWO CRYSTAL FORMS OF LENTIL LECTIN AT 1.8 ANGSTROMS RESOLUTION
Components(LECTIN) x 2
KeywordsLECTIN
Function / homology
Function and homology information


carbohydrate mediated signaling / mannose binding / manganese ion binding / carbohydrate binding / calcium 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 / Jelly Rolls ...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
: / PHOSPHATE ION / Lectin
Similarity search - Component
Biological speciesLens culinaris (lentil)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsVan Overberge, D. / Loris, R. / Wyns, L.
Citation
Journal: Proteins / Year: 1994
Title: Structural analysis of two crystal forms of lentil lectin at 1.8 A resolution.
Authors: Loris, R. / Van Overberge, D. / Dao-Thi, M.H. / Poortmans, F. / Maene, N. / Wyns, L.
#1: Journal: Biochemistry / Year: 1993
Title: Crystal Structure Determination and Refinement at 2.3 Angstroms Resolution of the Lentil Lectin
Authors: Loris, R. / Steyaert, J. / Maes, D. / Lisgarten, J. / Pickersgill, R. / Wyns, L.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Two Crystal Forms of the Lentil Lectin Diffract to High Resolution
Authors: Loris, R. / Lisgarten, J. / Maes, D. / Pickersgill, R. / Korber, F. / Reynolds, C. / Wyns, L.
History
DepositionNov 17, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Sep 9, 2020Group: Database references / Derived calculations
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._citation.title / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LECTIN
B: LECTIN
C: LECTIN
D: LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,62310
Polymers51,2434
Non-polymers3806
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17800 Å2
ΔGint-137 kcal/mol
Surface area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.490, 56.370, 82.730
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: ALA A 80 - ASP A 81 OMEGA =356.62 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ALA C 80 - ASP C 81 OMEGA =358.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein LECTIN /


Mass: 19906.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lens culinaris (lentil) / References: UniProt: P02870
#2: Protein LECTIN /


Mass: 5714.288 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lens culinaris (lentil) / References: UniProt: P02870

-
Non-polymers , 4 types, 237 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsEACH MONOMER HAS A BOUND CALCIUM, MANGANESE AMD PHOSPHATE ION. THE CALCIUM AND MANGANESE IONS ARE ...EACH MONOMER HAS A BOUND CALCIUM, MANGANESE AMD PHOSPHATE ION. THE CALCIUM AND MANGANESE IONS ARE ESSENTIAL FOR STABILIZING AN UNUSUAL ALA-ASP CIS PEPTIDE BOND, THAT IS AN ESSENTIAL FEATURE OF THE CARBOHYDRATE RECOGNITION SITE OF THIS LECTIN. THE PHOSPHATE IS BOUND IN THE CARBOHYDRATE RECOGNITION SITE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal grow
*PLUS
pH: 6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein11
220 mMphosphate11
320 mMacetate11pH6.0
435-40 %(v/v)MPD11

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.75 Å / Num. obs: 53882 / % possible obs: 83.7 % / Num. measured all: 169906 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 74.2 % / Rmerge(I) obs: 0.269

-
Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementRfactor obs: 0.175 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 14 231 3820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_deg7
Refinement
*PLUS
Rfactor obs: 0.175 / Rfactor Rwork: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg3
X-RAY DIFFRACTIONp_plane_restr0.013

+
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