[English] 日本語
Yorodumi
- PDB-4yld: The crystal structure of Sclerotium Rolfsii lectin variant 1 (SSR1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yld
TitleThe crystal structure of Sclerotium Rolfsii lectin variant 1 (SSR1)
ComponentsSclerotium Rolfsii lectin variant 1 (SSR1)
KeywordsSUGAR BINDING PROTEIN / Lectin / carbohydrate-binding specificity
Function / homologyFungal fruit body lectin / Fungal fruit body lectin / Cytolysin/lectin / Cytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta / Lectin
Function and homology information
Biological speciesAthelia rolfsii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKantsadi, A.L. / Peppa, V.I. / Leonidas, D.D.
CitationJournal: Molecules / Year: 2015
Title: Molecular Cloning, Carbohydrate Specificity and the Crystal Structure of Two Sclerotium rolfsii Lectin Variants.
Authors: Peppa, V.I. / Venkat, H. / Kantsadi, A.L. / Inamdar, S.R. / Bhat, G.G. / Eligar, S. / Shivanand, A. / Chachadi, V.B. / Satisha, G.J. / Swamy, B.M. / Skamnaki, V.T. / Zographos, S.E. / Leonidas, D.D.
History
DepositionMar 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sclerotium Rolfsii lectin variant 1 (SSR1)
B: Sclerotium Rolfsii lectin variant 1 (SSR1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2443
Polymers32,1252
Non-polymers1181
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-20 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.285, 100.285, 63.643
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-357-

HOH

-
Components

#1: Protein Sclerotium Rolfsii lectin variant 1 (SSR1)


Mass: 16062.690 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Athelia rolfsii (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KL30*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% v/v MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54178 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Feb 25, 2013
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→13.84 Å / Num. all: 36020 / Num. obs: 36020 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rsym value: 0.044 / Net I/σ(I): 24.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 5.5 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
CrysalisProdata reduction
SCALAdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→13.84 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.18 / Phase error: 15.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1793 1793 4.98 %
Rwork0.1467 --
obs0.1483 36020 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→13.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 8 398 2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142336
X-RAY DIFFRACTIONf_angle_d1.4493171
X-RAY DIFFRACTIONf_dihedral_angle_d14.345831
X-RAY DIFFRACTIONf_chiral_restr0.111336
X-RAY DIFFRACTIONf_plane_restr0.008416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74590.19091370.1612540X-RAY DIFFRACTION99
1.7459-1.79720.19031260.15482606X-RAY DIFFRACTION100
1.7972-1.8550.20951250.15442598X-RAY DIFFRACTION100
1.855-1.92120.19071240.15482607X-RAY DIFFRACTION100
1.9212-1.99790.18851490.15052593X-RAY DIFFRACTION100
1.9979-2.08850.20461180.14472616X-RAY DIFFRACTION100
2.0885-2.19820.1881640.1442597X-RAY DIFFRACTION100
2.1982-2.33530.18761360.14962607X-RAY DIFFRACTION100
2.3353-2.51460.17081550.15962616X-RAY DIFFRACTION100
2.5146-2.76590.18971370.15822654X-RAY DIFFRACTION100
2.7659-3.1620.20461420.15142654X-RAY DIFFRACTION100
3.162-3.96810.15121390.13412714X-RAY DIFFRACTION100
3.9681-13.84330.13991410.12922825X-RAY DIFFRACTION100

+
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