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- PDB-4z2f: Sclerotium Rolfsii lectin variant (SSR2) with fine carbohydrate s... -

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Basic information

Entry
Database: PDB / ID: 4z2f
TitleSclerotium Rolfsii lectin variant (SSR2) with fine carbohydrate specificity
Componentslectin variant 2
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 variant 2
Function and homology information
Biological speciesAthelia rolfsii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lectin variant 2
B: lectin variant 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4743
Polymers32,3562
Non-polymers1181
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-19 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.184, 100.184, 63.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein lectin variant 2 / SSR2


Mass: 16177.888 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: A0A0M3KL31*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.: 251 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5 / Details: 20% v/v MPD

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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: 1.6→13.56 Å / Num. obs: 43553 / % possible obs: 100 % / Redundancy: 5.6 % / Rsym value: 0.08 / Net I/σ(I): 16.3
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OFD

2ofd


Resolution: 2.5→13.56 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 553 4.76 %
Rwork0.1751 --
obs0.1784 11613 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→13.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 8 251 2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022346
X-RAY DIFFRACTIONf_angle_d0.5523183
X-RAY DIFFRACTIONf_dihedral_angle_d12.788835
X-RAY DIFFRACTIONf_chiral_restr0.041337
X-RAY DIFFRACTIONf_plane_restr0.002417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.74980.28111280.19172700X-RAY DIFFRACTION100
2.7498-3.14340.28011370.18922731X-RAY DIFFRACTION100
3.1434-3.94410.21981400.17042752X-RAY DIFFRACTION100
3.9441-13.57450.22971480.16032877X-RAY DIFFRACTION100

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