[English] 日本語
Yorodumi
- PDB-2ofe: The Crystal structure of Sclerotium rolfsii lectin in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ofe
TitleThe Crystal structure of Sclerotium rolfsii lectin in complex with N-acetyl-D-glucosamine
ComponentsSclerotium rolfsii lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / dual specificity
Function / homologyCytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesAthelia rolfsii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsLeonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Basis for the Carbohydrate Recognition of the Sclerotium rolfsii Lectin
Authors: Leonidas, D.D. / Swamy, B.M. / Hatzopoulos, G.N. / Gonchigar, S.J. / Chachadi, V.B. / Inamdar, S.R. / Zographos, S.E. / Oikonomakos, N.G.
History
DepositionJan 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP ...SEQUENCE AT THE TIME OF PROCESSING, THE SEQUENCE OF THIS PROTEIN IS NOT AVAILABLE AT THE UNP SEQUENCE DATABASE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sclerotium rolfsii lectin
B: Sclerotium rolfsii lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,15310
Polymers32,1792
Non-polymers9748
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-40 kcal/mol
Surface area12800 Å2
MethodPISA
2
A: Sclerotium rolfsii lectin
B: Sclerotium rolfsii lectin
hetero molecules

A: Sclerotium rolfsii lectin
B: Sclerotium rolfsii lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,30720
Polymers64,3594
Non-polymers1,94816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10030 Å2
ΔGint-94 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.768, 99.768, 64.080
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-1116-

HOH

21B-1161-

HOH

31B-1174-

HOH

DetailsThe Biological assembly of SRL is a dimer which is included in the asymmetric unit

-
Components

#1: Protein Sclerotium rolfsii lectin


Mass: 16089.714 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Athelia rolfsii (fungus)
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


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


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium acetate, 30 % MPD, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 34881 / Num. obs: 34881 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 8.994 Å2 / Rsym value: 0.055 / Net I/σ(I): 22.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 19 / Num. unique all: 1734 / Rsym value: 0.066 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2OFC

2ofc


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.436 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18407 1735 5 %RANDOM
Rwork0.15696 ---
obs0.15829 33108 96.92 %-
all-33108 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.093 Å0.097 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 66 379 2719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212416
X-RAY DIFFRACTIONr_angle_refined_deg1.021.9453279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.72324.375128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45315370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6881514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021854
X-RAY DIFFRACTIONr_nbd_refined0.1780.21059
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21625
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2358
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.247
X-RAY DIFFRACTIONr_mcbond_it0.5451.51448
X-RAY DIFFRACTIONr_mcangle_it0.89222252
X-RAY DIFFRACTIONr_scbond_it1.38831114
X-RAY DIFFRACTIONr_scangle_it2.1394.51027
LS refinement shellResolution: 1.7→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 121 -
Rwork0.17 2441 -
obs--98.42 %

+
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