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- PDB-1kj1: MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM)... -

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Basic information

Entry
Database: PDB / ID: 1kj1
TitleMANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE
Components
  • lectin I
  • lectin II
KeywordsPLANT PROTEIN / BULB LECTIN / MANNOSE
Function / homology
Function and homology information


response to other organism / carbohydrate binding
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
alpha-D-mannopyranose / II lectin / I lectin
Similarity search - Component
Biological speciesAllium sativum (garlic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRamachandraiah, G. / Chandra, N.R. / Surolia, A. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Re-refinement using reprocessed data to improve the quality of the structure: a case study involving garlic lectin.
Authors: Ramachandraiah, G. / Chandra, N.R. / Surolia, A. / Vijayan, M.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure of a Dimeric Mannose-Specific Agglutinin from Garlic: Quaternary Association and Carbohydrate Specificity
Authors: Chandra, N.R. / Ramachandraiah, G. / Bachhawat, K. / Dam, T.K. / Surolia, A. / Vijayan, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Crystallization and Preliminary Crystallographic Studies on the Mannose-Specific Lectin from Garlic
Authors: Chandra, N.R. / Dam, T.K. / Surolia, A. / Vijayan, M.
History
DepositionDec 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 16, 2023Group: 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lectin I
D: lectin II
P: lectin I
Q: lectin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,83818
Polymers48,3154
Non-polymers2,52214
Water3,153175
1
A: lectin I
D: lectin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4199
Polymers24,1582
Non-polymers1,2617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-4 kcal/mol
Surface area9780 Å2
MethodPISA
2
P: lectin I
Q: lectin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4199
Polymers24,1582
Non-polymers1,2617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-2 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.831, 43.516, 78.736
Angle α, β, γ (deg.)90.00, 112.26, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein lectin I / Mannose-Specific Agglutinin / LECGNA 1


Mass: 11988.233 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Allium sativum (garlic) / References: UniProt: Q38789
#2: Protein lectin II / Mannose-Specific Agglutinin / LECGNA 2


Mass: 12169.442 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Allium sativum (garlic) / References: UniProt: Q38783
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS, 1WEEK, pH 7.00, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
Temperature: 294 K / pH: 7
Details: Chandra, N.R., (1997) Acta Crystallogr., Sect.D, 53, 787.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.5 mg/mlprotein1drop
220 mMphosphate-buffered saline1drop
320 %(w/v)PEG80001reservoir
420 mMphosphate-buffered saline1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 29430 / % possible obs: 90.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1791 / % possible all: 55.8
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / Num. measured all: 102203
Reflection shell
*PLUS
% possible obs: 55.8 % / Num. unique obs: 1791

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SNOWDROP LECTIN (PDB ENTRY 1MSA)

1msa


Resolution: 2.2→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 245621.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2649 9.7 %RANDOM
Rwork0.211 ---
obs0.211 27423 84.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.3531 Å2 / ksol: 0.330189 e/Å3
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1--13.41 Å20 Å2-3.83 Å2
2--15.4 Å20 Å2
3----1.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 168 175 3745
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 256 9.2 %
Rwork0.334 2538 -
obs--52.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.73
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.37 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.334

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