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

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Basic information

Entry
Database: PDB / ID: 1jpc
TitleMANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM SNOWDROP (GALANTHUS NIVALIS) BULBS IN COMPLEX WITH MANNOSE-ALPHA1,6-(MANNOSE-ALPHA1,3)-MANNOSE-ALPHA1,6-(MANNOSE-ALPHA1,3)-MANNOSE
ComponentsAGGLUTININ
KeywordsLECTIN / AGGLUTININ / MANNOPENTAOSE / (MANNOSE-ALPHA1 / 6-(MANNOSE-ALPHA1 / 3-MANNOSE- ALPHA1 / 3)-MANNOSE) / SNOWDROP
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
6alpha-alpha-mannobiose / Mannose-specific lectin
Similarity search - Component
Biological speciesGalanthus nivalis (common snowdrop)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsWright, C.S. / Hester, G.
Citation
Journal: Structure / Year: 1996
Title: The 2.0 A structure of a cross-linked complex between snowdrop lectin and a branched mannopentaose: evidence for two unique binding modes.
Authors: Wright, C.S. / Hester, G.
#1: 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.
#2: 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
DepositionJul 30, 1996Processing site: BNL
Revision 1.0Jan 27, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 5, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: chem_comp / pdbx_distant_solvent_atoms ...chem_comp / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_conn
Item: _chem_comp.type / _pdbx_struct_assembly_prop.biol_id ..._chem_comp.type / _pdbx_struct_assembly_prop.biol_id / _software.name / _struct_conn.pdbx_leaving_atom_flag
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 / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4134
Polymers12,0611
Non-polymers1,3513
Water99155
1
A: AGGLUTININ
hetero molecules

A: AGGLUTININ
hetero molecules

A: AGGLUTININ
hetero molecules

A: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,65016
Polymers48,2454
Non-polymers5,40512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area14000 Å2
ΔGint31 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.339, 96.339, 68.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-132-

HOH

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Components

#1: Protein AGGLUTININ / SNOWDROP LECTIN


Mass: 12061.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE SNOWDROP IS A REPRESENTATIVE OF THE PLANT FAMILY OF AMARYLLIDACEAE. THE PROTEIN IS ISOLATED FROM THE BULBS.
Source: (natural) Galanthus nivalis (common snowdrop) / References: UniProt: P30617
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose / 6alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 6alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(6+1)][a-D-Manp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 57 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
133 %satammonium salfate1reservoir
20.05 Mammonium bicarbonate1reservoir
33.5 mg/mlprotein1drop
40.28 mMMan-51drop
59 %ammonium sulfate1drop

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 7, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 11166 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.074
Reflection
*PLUS
Num. measured all: 54560
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.05 Å / % possible obs: 99.6 %

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Processing

Software
NameVersionClassification
MOSFLM5.23data reduction
SCALAdata scaling
Agrovatadata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
X-PLOR3.1phasing
RefinementResolution: 2→8 Å / σ(F): 0
RfactorNum. reflection
Rfree0.22 -
Rwork0.187 -
obs0.187 11166
Displacement parametersBiso mean: 33.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 91 55 989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.43
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.36
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.118
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: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.36
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.118

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