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- PDB-1c3n: CRYSTAL STRUCTURE OF HELIANTHUS TUBEROSUS LECTIN COMPLEXED TO MAN... -

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Basic information

Entry
Database: PDB / ID: 1c3n
TitleCRYSTAL STRUCTURE OF HELIANTHUS TUBEROSUS LECTIN COMPLEXED TO MAN(1-2)MAN
ComponentsAGGLUTININ
KeywordsSUGAR BINDING PROTEIN / AGGLUTININ / BETA-PRISM / MANNOSE / JACALIN-RELATED
Function / homology
Function and homology information


carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
2alpha-alpha-mannobiose / : / Lectin 1
Similarity search - Component
Biological speciesHelianthus tuberosus (Jerusalem artichoke)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsBourne, Y. / Zamboni, V. / Barre, A. / Peumans, W.J. / van Damme, E.J.M. / Rouge, P.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Helianthus tuberosus lectin reveals a widespread scaffold for mannose-binding lectins.
Authors: Bourne, Y. / Zamboni, V. / Barre, A. / Peumans, W.J. / Van Damme, E.J. / Rouge, P.
History
DepositionJul 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
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.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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8442
Polymers15,5011
Non-polymers3421
Water1,58588
1
A: AGGLUTININ
hetero molecules

A: AGGLUTININ
hetero molecules

A: AGGLUTININ
hetero molecules

A: AGGLUTININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3758
Polymers62,0064
Non-polymers1,3694
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation10_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
2
A: AGGLUTININ
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)126,75016
Polymers124,0128
Non-polymers2,7388
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area18060 Å2
ΔGint-24 kcal/mol
Surface area43090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.767, 104.767, 64.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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Components

#1: Protein AGGLUTININ


Mass: 15501.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TUBER
Source: (natural) Helianthus tuberosus (Jerusalem artichoke)
References: GenBank: AAD11575, UniProt: Q9ZQY5*PLUS
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-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: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 26-28% PEG MONOMETHYL ESTER 0.2 M MAGNESIUM ACETATE, pH 7.0, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.5 mg/mlprotein1drop
210 mMHEPES1drop
3150 mM1dropNaCl
43 mMEDTA1drop
50.005 %p201drop
626-28 %mPEG5501reservoir
70.2 Mcalcium acetate1reservoiror magnesium acetate
80.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→12 Å / Num. obs: 6269 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.1
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.35 / % possible all: 93.3
Reflection
*PLUS
Num. measured all: 53576
Reflection shell
*PLUS
% possible obs: 91.7 % / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2.45→12 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.243 353 -RANDOM
Rwork0.186 ---
obs0.186 5916 92.3 %-
Refinement stepCycle: LAST / Resolution: 2.45→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1077 0 23 88 1188
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 6269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_deg1.08

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