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- PDB-3miv: Structure of Banana lectin - Glc-alpha(1,2)-Glc complex -

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Basic information

Entry
Database: PDB / ID: 3miv
TitleStructure of Banana lectin - Glc-alpha(1,2)-Glc complex
ComponentsLectin
KeywordsSUGAR BINDING PROTEIN / ALL BETA SHEET PROTEIN / BETA PRISM-I FOLD / MANNOSE SPECIFIC
Function / homology
Function and homology information


carbohydrate binding / metal ion 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 speciesMusa acuminata (dwarf banana)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSharma, A. / Vijayan, M.
CitationJournal: Glycobiology / Year: 2011
Title: Influence of glycosidic linkage on the nature of carbohydrate binding in beta-prism I fold lectins: an X-ray and molecular dynamics investigation on banana lectin-carbohydrate complexes
Authors: Sharma, A. / Vijayan, M.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4323
Polymers29,3672
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-11 kcal/mol
Surface area12350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.569, 82.569, 149.446
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Lectin


Mass: 14683.493 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Musa acuminata (dwarf banana) / References: UniProt: Q8L5H4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 5.01 Å3/Da / Density % sol: 75.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ZINC ACETATE DIHYDRATE, SODIUM CACODYLATE, 1,6-HEXANEDIOL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 5, 2004 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.5→10 Å / Num. all: 7895 / Num. obs: 6751 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.9
Reflection shellResolution: 3.5→3.62 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.8 / Num. unique all: 672 / % possible all: 91.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1x1v

1x1v


Resolution: 3.5→9.99 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.847 / SU B: 24.238 / SU ML: 0.396 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 669 9.9 %RANDOM
Rwork0.21738 ---
obs0.22193 6056 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.603 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å21.72 Å20 Å2
2--3.45 Å20 Å2
3----5.17 Å2
Refinement stepCycle: LAST / Resolution: 3.5→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 1 0 2033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222086
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9442818
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43323.49483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.73715295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.624156
X-RAY DIFFRACTIONr_chiral_restr0.0770.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021636
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2848
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21382
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0440.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2750.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4641.51366
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.83722122
X-RAY DIFFRACTIONr_scbond_it0.7983823
X-RAY DIFFRACTIONr_scangle_it1.364.5696
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.501→3.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 49 -
Rwork0.254 421 -
obs--100 %

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