[English] 日本語
Yorodumi
- PDB-8szo: Canavalia villosa lectin in complex with alpha-methyl-mannoside -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8szo
TitleCanavalia villosa lectin in complex with alpha-methyl-mannoside
ComponentsCanavalia villosa lectin
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding protein / Plant lectin / beta-sandwich / pro-inflammatory / PLANT PROTEIN
Function / homologymethyl alpha-D-mannopyranoside / :
Function and homology information
Biological speciesCanavalia villosa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCavada, B.S. / Lossio, C.F. / Pinto-Junior, V.R. / Osterne, V.J.S. / Oliveira, M.V. / Neco, A.H.B. / Nascimento, K.S.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
Coordination for the Improvement of Higher Education Personnel Brazil
CitationJournal: Int J Biol Macromol / Year: 2017
Title: Lectin from Canavalia villosa seeds: A glucose/mannose-specific protein and a new tool for inflammation studies.
Authors: Lossio, C.F. / Moreira, C.G. / Amorim, R.M.F. / Nobre, C.S. / Silva, M.T.L. / Neto, C.C. / Pinto-Junior, V.R. / Silva, I.B. / Campos, J. / Assreuy, A.M.S. / Cavada, B.S. / Nascimento, K.S.
History
DepositionMay 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Canavalia villosa lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0675
Polymers25,6851
Non-polymers3814
Water1,58588
1
A: Canavalia villosa lectin
hetero molecules

A: Canavalia villosa lectin
hetero molecules

A: Canavalia villosa lectin
hetero molecules

A: Canavalia villosa lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,26720
Polymers102,7424
Non-polymers1,52516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area10130 Å2
ΔGint-105 kcal/mol
Surface area33970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.490, 84.440, 89.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Canavalia villosa lectin


Mass: 25685.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The residues S117, N118, S119 and T120 in the coordinate sequence are located in a loop region of the tertiary structure and were not detected due to lack of electron density on this ...Details: The residues S117, N118, S119 and T120 in the coordinate sequence are located in a loop region of the tertiary structure and were not detected due to lack of electron density on this specific region. This data deficiency is frequently observed in other ConA-like lectins structures solved by macromolecular crystallography. The sample sequence displays the full 237 amino acid of the protein.
Source: (natural) Canavalia villosa (plant)
#4: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 91 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.2
Details: PEG1000, potassium citrate phosphate, lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.5→27.48 Å / Num. obs: 8301 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.056 / Rrim(I) all: 0.126 / Net I/σ(I): 8.9 / Num. measured all: 40674
Reflection shellResolution: 2.5→2.64 Å / % possible obs: 99.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.433 / Num. measured all: 5399 / Num. unique obs: 1200 / CC1/2: 0.867 / Rpim(I) all: 0.224 / Rrim(I) all: 0.489 / Net I/σ(I) obs: 3

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→27.48 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2489 408 4.92 %
Rwork0.1813 --
obs0.1848 8295 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 21 88 1893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091847
X-RAY DIFFRACTIONf_angle_d0.9982518
X-RAY DIFFRACTIONf_dihedral_angle_d13.951650
X-RAY DIFFRACTIONf_chiral_restr0.057294
X-RAY DIFFRACTIONf_plane_restr0.009323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.640.29761200.22222604X-RAY DIFFRACTION100
2.64-3.60.2861390.20292602X-RAY DIFFRACTION100
3.6-27.480.2211490.15952681X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 14.6292 Å / Origin y: 14.4776 Å / Origin z: 11.3444 Å
111213212223313233
T0.2167 Å2-0.0522 Å2-0.0287 Å2-0.2166 Å2-0.0575 Å2--0.2272 Å2
L1.0932 °2-0.4264 °20.3622 °2-1.4682 °2-0.1789 °2--0.9354 °2
S0.0087 Å °-0.0128 Å °0.033 Å °0.1654 Å °0.0568 Å °-0.1773 Å °-0.0992 Å °0.0416 Å °0.0001 Å °
Refinement TLS groupSelection details: all

+
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