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- PDB-1msa: MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIV... -

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Basic information

Entry
Database: PDB / ID: 1msa
TitleMANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS COMPLEXED WITH METHYL-ALPHA-D-MANNOSIDE
ComponentsAGGLUTININ
KeywordsLECTIN (AGGLUTININ) / METHYL-ALPHA-D-MANNOSIDE
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / response to virus / extracellular region
Similarity search - Function
Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / Mannose-specific lectin
Similarity search - Component
Biological speciesGalanthus nivalis (common snowdrop)
MethodX-RAY DIFFRACTION / Resolution: 2.29 Å
AuthorsWright, C.S. / Hester, G.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Structure of mannose-specific snowdrop (Galanthus nivalis) lectin is representative of a new plant lectin family.
Authors: Hester, G. / Kaku, H. / Goldstein, I.J. / Wright, C.S.
#1: Journal: Eur.J.Biochem. / Year: 1991
Title: Biosynthesis, Primary Structure and Molecular Cloning of Snowdrop (Galanthus Nivalis) Lectin
Authors: Van Damme, E.J.M. / Kaku, H. / Perini, F. / Goldstein, I.J. / Peeters, B. / Yagi, F. / Decock, B. / Peumans, W.J.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Crystallization and Preliminary X-Ray Diffraction Results of Snowdrop (Galanthus Nivalis) Lectin
Authors: Wright, C.S. / Kaku, H. / Goldstein, I.J.
History
DepositionMar 6, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGGLUTININ
B: AGGLUTININ
C: AGGLUTININ
D: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,57616
Polymers48,2454
Non-polymers2,33012
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-21 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.820, 64.110, 62.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: GLY A 98 - THR A 99 OMEGA = 359.12 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: GLY B 98 - THR B 99 OMEGA = 0.90 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: GLY C 98 - THR C 99 OMEGA = 357.74 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: GLY D 98 - THR D 99 OMEGA = 0.32 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9276, 0.0673, 0.3675), (0.0852, -0.9197, 0.3834), (0.3638, 0.3869, 0.8473)138.12891, 58.3432, -39.4103
2given(-0.7148, 0.6717, -0.1946), (0.6718, 0.5821, -0.4581), (-0.1944, -0.4582, -0.8673)118.021, -18.3564, 109.0937
3given(0.6486, -0.7409, -0.1745), (-0.7414, -0.6668, 0.0754), (-0.1722, 0.0805, -0.9818)66.3521, 126.7221, 89.1897
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 1 .. A 109 B 1 .. B 109 0.360 M2 A 1 .. A 109 C 1 .. C 109 0.507 M3 A 1 .. A 109 D 1 .. D 109 0.568

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Components

#1: Protein
AGGLUTININ / SNOWDROP LECTIN


Mass: 12061.348 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Galanthus nivalis (common snowdrop) / References: UniProt: P30617
#2: Sugar
ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Source detailsMOLECULE_NAME: GALANTHUS NIVALIS AGGLUTININ. THE SNOWDROP IS A REPRESENTATIVE OF THE PLANT FAMILY ...MOLECULE_NAME: GALANTHUS NIVALIS AGGLUTININ. THE SNOWDROP IS A REPRESENTATIVE OF THE PLANT FAMILY OF AMARYLLIDACEAE. THE PROTEIN IS ISOLATED FROM THE BULBS.

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal grow
*PLUS
pH: 8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
145 %ammonium sulfate11
20.5-1.0 MMe-alpha-Man11

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorDetector: AREA DETECTOR / Date: Feb 20, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 23359 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Rmerge(I) obs: 0.044
Reflection
*PLUS
Highest resolution: 2.295 Å / Rmerge(I) obs: 0.044

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Processing

Software
NameVersionClassification
SOFTWAREPROVIDED BY MAXDdata collection
X-PLOR3model building
X-PLOR3refinement
SOFTWAREPROVIDED BY MAXDdata reduction
X-PLOR3phasing
RefinementResolution: 2.29→8 Å / σ(F): 0
Details: THREONINE 99 HAS A PEPTIDE TORSION ANGLE WITH A CIS CONFORMATION. IN THE TOPOLOGY AND PARAMETER FILES USED FOR REFINEMENT A NEW RESIDUE CALLED CTH WAS INTRODUCED. THIS IS A THR RESIDUE WITH ...Details: THREONINE 99 HAS A PEPTIDE TORSION ANGLE WITH A CIS CONFORMATION. IN THE TOPOLOGY AND PARAMETER FILES USED FOR REFINEMENT A NEW RESIDUE CALLED CTH WAS INTRODUCED. THIS IS A THR RESIDUE WITH A NEW ATOM TYPE BEING A MAIN CHAIN NITROGEN ATOM WHICH IS INVOLVED IN A CIS PEPTIDE BOND.
RfactorNum. reflection% reflection
Rfree0.24 --
Rwork0.177 --
obs0.177 22685 91.5 %
Displacement parametersBiso mean: 18.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.29→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 156 327 3875
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.575
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.065
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.295 Å / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_dihedral_angle_d / Dev ideal: 27.24

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