[English] 日本語
Yorodumi
- PDB-4ndt: Crystal structure of L. decastes alpha-galactosyl-binding lectin,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ndt
TitleCrystal structure of L. decastes alpha-galactosyl-binding lectin, orthorhombic crystal form
ComponentsAlpha-galactosyl-binding lectin
KeywordsSUGAR BINDING PROTEIN / lectin
Function / homology: / Alpha-galactosyl binding lectin / galactose binding / Alpha-galactosyl-binding lectin
Function and homology information
Biological speciesLyophyllum decastes (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.03 Å
AuthorsVan Eerde, A. / Grahn, E. / Krengel, U.
CitationJournal: Glycobiology / Year: 2015
Title: Atomic-resolution structure of the alpha-galactosyl binding Lyophyllum decastes lectin reveals a new protein family found in both fungi and plants.
Authors: van Eerde, A. / Grahn, E.M. / Winter, H.C. / Goldstein, I.J. / Krengel, U.
History
DepositionOct 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Alpha-galactosyl-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3872
Polymers10,2911
Non-polymers961
Water3,603200
1
A: Alpha-galactosyl-binding lectin
hetero molecules

A: Alpha-galactosyl-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7754
Polymers20,5832
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2290 Å2
ΔGint-33 kcal/mol
Surface area8350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.365, 44.230, 62.133
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

-
Components

#1: Protein Alpha-galactosyl-binding lectin


Mass: 10291.380 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lyophyllum decastes (fungus) / Organ: fruiting bodiesSporocarp (fungi) / References: UniProt: A7UNK4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.03→20 Å / Num. all: 50532 / Num. obs: 50528 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 7.38 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.93
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.03-1.090.591.61186.6
1.09-1.170.3364.15199.9
1.17-1.260.2386.25199.9
1.26-1.380.1619.09199.9
1.38-1.540.114.11199.7
1.54-1.780.06321.11199.8
1.78-2.180.04230.09199.3
2.18-3.080.03437.12199
3.080.02941.04196.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NDS

4nds


Resolution: 1.03→18.756 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.07 / σ(F): 1.99 / Phase error: 11.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1352 2531 5.02 %
Rwork0.1142 --
obs0.1152 50408 97.55 %
all-50528 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.078 Å2
Refinement stepCycle: LAST / Resolution: 1.03→18.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms722 0 5 200 927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01842
X-RAY DIFFRACTIONf_angle_d1.481149
X-RAY DIFFRACTIONf_dihedral_angle_d12.771311
X-RAY DIFFRACTIONf_chiral_restr0.083116
X-RAY DIFFRACTIONf_plane_restr0.009158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.03-1.04980.311040.26212120X-RAY DIFFRACTION79
1.0498-1.07130.24951230.22952356X-RAY DIFFRACTION88
1.0713-1.09450.23561350.19492554X-RAY DIFFRACTION95
1.0945-1.120.14791410.16312685X-RAY DIFFRACTION100
1.12-1.1480.16591410.13312699X-RAY DIFFRACTION100
1.148-1.1790.15731400.12032699X-RAY DIFFRACTION100
1.179-1.21370.14221530.11482693X-RAY DIFFRACTION100
1.2137-1.25290.1561380.11452693X-RAY DIFFRACTION100
1.2529-1.29770.11821330.10472723X-RAY DIFFRACTION100
1.2977-1.34960.11631290.08832711X-RAY DIFFRACTION100
1.3496-1.4110.12861570.08832692X-RAY DIFFRACTION100
1.411-1.48540.10621430.0822720X-RAY DIFFRACTION100
1.4854-1.57840.1081580.0782693X-RAY DIFFRACTION100
1.5784-1.70020.10431460.07962738X-RAY DIFFRACTION100
1.7002-1.87120.10321390.08582732X-RAY DIFFRACTION100
1.8712-2.14160.10371510.0892730X-RAY DIFFRACTION99
2.1416-2.69690.12661440.11062778X-RAY DIFFRACTION99
2.6969-18.75960.15051560.13442861X-RAY DIFFRACTION98

+
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