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- PDB-2ofd: The Crystal Structure of Sclerotium rolfsii lectin in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2ofd
TitleThe Crystal Structure of Sclerotium rolfsii lectin in complex with N-acetyl-D-galactosamine
ComponentsSclerotium rolfsii lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / dual specificity
Function / homologyCytolysin/lectin / Mutm (Fpg) Protein; Chain: A, domain 2 / Sandwich / Mainly Beta / ACETATE ION / 2-acetamido-2-deoxy-beta-D-galactopyranose
Function and homology information
Biological speciesAthelia rolfsii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.96 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: 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999 SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,0208
Polymers32,1792
Non-polymers8416
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-9 kcal/mol
Surface area12920 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)66,04016
Polymers64,3594
Non-polymers1,68212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9900 Å2
ΔGint-32 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.485, 99.485, 64.007
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe Biological assembly of SRL is a dimer and it is included in the asymmetric unit

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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-NGA / 2-acetamido-2-deoxy-beta-D-galactopyranose / N-acetyl-beta-D-galactosamine / 2-acetamido-2-deoxy-beta-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-D-GALACTOSAMINE


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


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.01 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8128 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8128 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. all: 22675 / Num. obs: 22675 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 17.3 Å2 / Rsym value: 0.039 / Net I/σ(I): 18.2
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.178 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 2OFC

2ofc


Resolution: 1.96→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.951 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19299 1171 5.2 %RANDOM
Rwork0.16102 ---
obs0.16262 21504 96.49 %-
all-21504 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.252 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.134 Å0.153 Å
Refinement stepCycle: LAST / Resolution: 1.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 57 193 2524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212380
X-RAY DIFFRACTIONr_angle_refined_deg1.051.9293228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.0224.375128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60415370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8261514
X-RAY DIFFRACTIONr_chiral_restr0.080.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021850
X-RAY DIFFRACTIONr_nbd_refined0.1770.2894
X-RAY DIFFRACTIONr_nbtor_refined0.30.21586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.221
X-RAY DIFFRACTIONr_mcbond_it0.5261.51462
X-RAY DIFFRACTIONr_mcangle_it0.89622252
X-RAY DIFFRACTIONr_scbond_it1.35731078
X-RAY DIFFRACTIONr_scangle_it2.0754.5976
LS refinement shellResolution: 1.96→2.015 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 76 -
Rwork0.179 1294 -
obs--79.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63690.10930.35440.6775-0.03461.02110.0464-0.0334-0.02040.0033-0.0029-0.01510.08320.025-0.0435-0.00660.0069-0.006-0.0569-0.0048-0.010831.465.515728.9798
20.5275-0.14370.17520.4410.08540.8058-0.0151-0.0026-0.0208-0.05810.02840.014-0.06380.008-0.0133-0.0012-0.00740.0128-0.0367-0.0035-0.025727.361123.731313.7325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1411 - 142
2X-RAY DIFFRACTION2BB0 - 1411 - 142

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