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

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Basic information

Entry
Database: PDB / ID: 1niv
TitleMANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA 1,3-METHYL-D-MANNOSE
ComponentsAGGLUTININ
KeywordsLECTIN / MANNOSE-BINDING
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / response to virus / defense response / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWright, C.S. / Hester, G.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: The mannose-specific bulb lectin from Galanthus nivalis (snowdrop) binds mono- and dimannosides at distinct sites. Structure analysis of refined complexes at 2.3 A and 3.0 A resolution.
Authors: Hester, G. / Wright, C.S.
#1: 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.
History
DepositionMar 15, 1996Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 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: AGGLUTININ
C: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7748
Polymers24,1232
Non-polymers1,6526
Water00
1
A: AGGLUTININ
C: AGGLUTININ
hetero molecules

A: AGGLUTININ
C: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54816
Polymers48,2454
Non-polymers3,30312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_755-x+2,-y+1/2,z1
Unit cell
Length a, b, c (Å)138.149, 138.149, 138.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.6624, 0.7492, -0.0051), (0.7492, -0.6623, 0.0072), (0.002, -0.0086, -1)
Vector: 21.4768, -47.0425, 256.26071)

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Components

#1: Protein AGGLUTININ / SNOWDROP LECTIN


Mass: 12061.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: THE SNOWDROP IS A REPRESENTATIVE OF THE PLANT FAMILY OF AMARYLLIDACEAE
Source: (natural) Galanthus nivalis (common snowdrop) / Organ: BULB / References: UniProt: P30617
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: 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.: 3
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.55 Å3/Da / Density % sol: 68 %
Crystal grow
*PLUS
pH: 8.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein11
20.05 Mammonium bicarbonate11
30.023 MMeMan-211

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 9, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 8280 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 9
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.9 / % possible all: 86.3
Reflection
*PLUS
Num. measured all: 39125
Reflection shell
*PLUS
% possible obs: 86.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GNA-ALPHA-MEMAN COMPLEX

Resolution: 3→8 Å / σ(F): 0
Details: THE MEAN B-FACTORS OF CHAINS A AND C ARE 22.5 AND 41.7 A**2, RESPECTIVELY. CHAIN C IS VERY FLEXIBLE DUE TO A LACK OF CRYSTAL CONTACTS.
RfactorNum. reflection% reflection
Rfree0.269 -7 %
Rwork0.227 --
obs0.227 7779 93.1 %
Displacement parametersBiso mean: 32.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 111 0 1799
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.527
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.05
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.127
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 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.227 / Rfactor obs: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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