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- PDB-1c3k: CRYSTAL STRUCTURE OF HELIANTHUS TUBEROSUS LECTIN -

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Basic information

Entry
Database: PDB / ID: 1c3k
TitleCRYSTAL STRUCTURE OF HELIANTHUS TUBEROSUS LECTIN
ComponentsAGGLUTININ
KeywordsSUGAR BINDING PROTEIN / BETA PRISM / AGGLUTININ / JACALIN-RELATED / MANNOSE
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
Biological speciesHelianthus tuberosus (Jerusalem artichoke)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AGGLUTININ


Theoretical massNumber of molelcules
Total (without water)15,5011
Polymers15,5011
Non-polymers00
Water2,126118
1
A: AGGLUTININ

A: AGGLUTININ

A: AGGLUTININ

A: AGGLUTININ


Theoretical massNumber of molelcules
Total (without water)62,0064
Polymers62,0064
Non-polymers00
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
x 8


Theoretical massNumber of molelcules
Total (without water)124,0128
Polymers124,0128
Non-polymers00
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 area12900 Å2
ΔGint-61 kcal/mol
Surface area43590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.927, 104.927, 63.751
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-169-

HOH

21A-223-

HOH

31A-250-

HOH

41A-264-

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: UniProt: Q9ZQY5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 26-28% PEG MONOMETHYL ESTER 550, 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.835
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.835 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 11028 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.233 / % possible all: 91.2
Reflection
*PLUS
Num. measured all: 86459
Reflection shell
*PLUS
% possible obs: 92.3 % / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.255 570 -RANDOM
Rwork0.2 ---
obs0.2 10459 89.4 %-
all-11029 --
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1071 0 0 118 1189
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
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_deg1.7
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 all: 11024 / % reflection Rfree: 5 % / Rfactor all: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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