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- PDB-4z2q: The crystal structure of Sclerotium Rolfsii lectin variant 1 (SSR... -

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Basic information

Entry
Database: PDB / ID: 4z2q
TitleThe crystal structure of Sclerotium Rolfsii lectin variant 1 (SSR1) in complex with N-acetyl-glucosamine
ComponentsLectin
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 / 2-acetamido-2-deoxy-alpha-D-glucopyranose / Lectin
Function and homology information
Biological speciesAthelia rolfsii (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3699
Polymers32,1252
Non-polymers1,2437
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-2 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.919, 99.919, 63.810
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-438-

HOH

21B-456-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lectin


Mass: 16062.690 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Athelia rolfsii (fungus) / Gene: l1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M3KL30*PLUS

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Sugars , 2 types, 4 molecules

#3: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: 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


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

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Non-polymers , 3 types, 401 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% v/v MPD

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 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: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→13.83 Å / Num. obs: 25956 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rsym value: 0.089 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 5.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
CrysalisProdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OFE

2ofe


Resolution: 1.9→13.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.518 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 1323 5.1 %RANDOM
Rwork0.14566 ---
obs0.14762 24633 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.541 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: 1 / Resolution: 1.9→13.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2268 0 84 398 2750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192401
X-RAY DIFFRACTIONr_bond_other_d0.0020.022180
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9383261
X-RAY DIFFRACTIONr_angle_other_deg1.74334978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6675280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.03824.375128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53915370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4611514
X-RAY DIFFRACTIONr_chiral_restr0.2240.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02620
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6460.6921127
X-RAY DIFFRACTIONr_mcbond_other0.6350.691125
X-RAY DIFFRACTIONr_mcangle_it1.1141.0321404
X-RAY DIFFRACTIONr_mcangle_other1.1131.0321405
X-RAY DIFFRACTIONr_scbond_it0.890.7941274
X-RAY DIFFRACTIONr_scbond_other0.890.7941275
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.491.1621858
X-RAY DIFFRACTIONr_long_range_B_refined5.3237.2693090
X-RAY DIFFRACTIONr_long_range_B_other5.3237.2723091
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.199 111 -
Rwork0.181 1789 -
obs--99.79 %

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