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

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Basic information

Entry
Database: PDB / ID: 1bwu
TitleMANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE
Components(PROTEIN (AGGLUTININ)) x 4
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: 2.8 Å
AuthorsChandra, N.R. / Ramachandraiah, G. / Bachhawat, K. / Dam, T.K. / Surolia, A. / Vijayan, M.
Citation
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.
#1: 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
DepositionSep 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 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 1.5Aug 9, 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 1.6Oct 9, 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: PROTEIN (AGGLUTININ)
D: PROTEIN (AGGLUTININ)
P: PROTEIN (AGGLUTININ)
Q: PROTEIN (AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,20118
Polymers47,6784
Non-polymers2,52214
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: PROTEIN (AGGLUTININ)
Q: PROTEIN (AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9509
Polymers23,6892
Non-polymers1,2617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-3 kcal/mol
Surface area10610 Å2
MethodPISA, PQS
3
A: PROTEIN (AGGLUTININ)
D: PROTEIN (AGGLUTININ)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2509
Polymers23,9892
Non-polymers1,2617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint1 kcal/mol
Surface area9820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)203.243, 43.780, 79.268
Angle α, β, γ (deg.)90.00, 112.37, 90.00
Int Tables number5
Space group name H-MC121
DetailsSUBUNITS, CHAINS A AND D and CHAINS P AND Q, FORM 2 INDEPENDENT HETERO-DIMERS IN THE ASYMMETRIC UNIT

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Components

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Protein , 4 types, 4 molecules ADPQ

#1: Protein PROTEIN (AGGLUTININ) / GARLIC LECTIN


Mass: 11865.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allium sativum (garlic) / References: UniProt: Q38789
#2: Protein PROTEIN (AGGLUTININ) / GARLIC LECTIN


Mass: 12124.300 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allium sativum (garlic) / References: UniProt: Q38784
#3: Protein PROTEIN (AGGLUTININ) / GARLIC LECTIN


Mass: 11678.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allium sativum (garlic) / References: UniProt: Q38789
#4: Protein PROTEIN (AGGLUTININ) / GARLIC LECTIN


Mass: 12010.171 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allium sativum (garlic) / References: UniProt: Q38784

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Sugars / Non-polymers , 2 types, 151 molecules

#5: 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: obtained synthetically / 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.58 Å3/Da / Density % sol: 65.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG8000, 5.5 MG/ML PROTEIN, 10MM MANNOSE, 20MM PBS PH 7.0, 1 WEEK, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 294 K
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 / Wavelength: 1.54
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: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→9 Å / Num. obs: 22244 / % possible obs: 86.6 % / Redundancy: 2.31 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.552.20.369112.2
2.55-2.80.2261
Reflection shell
*PLUS
% possible obs: 12.2 %

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Processing

Software
NameVersionClassification
XDSdata scaling
AUTOMARdata reduction
AMoREphasing
X-PLOR3.851refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SNOWDROP LECTIN (PDB ENTRY 1MSA)

1msa


Resolution: 2.8→9 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 770 7.2 %RANDOM
Rwork0.226 ---
obs0.226 10693 58.7 %-
Displacement parametersBiso mean: 32.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.54 Å
Refinement stepCycle: LAST / Resolution: 2.8→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3359 0 168 137 3664
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
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
LS refinement shellResolution: 2.55→2.8 Å / Rfactor Rfree error: 0.099 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.534 29 6 %
Rwork0.426 451 -
obs--35.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO
X-RAY DIFFRACTION3PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.534 / % reflection Rfree: 6 % / Rfactor Rwork: 0.426

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