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- PDB-3miu: Structure of Banana Lectin-pentamannose complex -

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Basic information

Entry
Database: PDB / ID: 3miu
TitleStructure of Banana Lectin-pentamannose 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 / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
3alpha-alpha-mannobiose / HEXANE-1,6-DIOL / alpha-D-mannopyranose / Lectin
Similarity search - Component
Biological speciesMusa acuminata (dwarf banana)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.63 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 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lectin
B: Lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,32314
Polymers29,3672
Non-polymers1,95612
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-12 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.911, 80.911, 147.405
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-179-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#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

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Sugars , 2 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{}}LINUCSPDB-CARE
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
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

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Non-polymers , 3 types, 80 molecules

#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 4.74 Å3/Da / Density % sol: 74.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: ZINC ACETATE DIHYDRATE, SODIUM CACODYLATE, 1,6-HEXANEDIOL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 8, 2005 / 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: 2.63→30 Å / Num. all: 17203 / Num. obs: 17137 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 8.76 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 33
Reflection shellResolution: 2.63→2.72 Å / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1646 / % possible all: 98.7

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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: 2.63→24.92 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 16.908 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24335 1320 7.7 %RANDOM
Rwork0.21667 ---
obs0.21875 15770 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: 57.022 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å21.87 Å20 Å2
2--3.74 Å20 Å2
3----5.61 Å2
Refinement stepCycle: LAST / Resolution: 2.63→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 121 74 2225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222216
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9982995
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67723.33384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96615291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.777156
X-RAY DIFFRACTIONr_chiral_restr0.0790.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021656
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.2912
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.21483
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0040.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.361.51369
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.6822130
X-RAY DIFFRACTIONr_scbond_it0.9833949
X-RAY DIFFRACTIONr_scangle_it1.724.5865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.632→2.7 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 95 -
Rwork0.363 1125 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 25.8975 Å / Origin y: 23.0138 Å / Origin z: 58.2078 Å
111213212223313233
T-0.2378 Å20.0427 Å20.0525 Å2--0.3221 Å2-0.0259 Å2---0.2166 Å2
L1.9969 °2-1.4149 °20.7178 °2-2.2242 °2-0.2923 °2--7.5815 °2
S0.1278 Å °-0.0794 Å °-0.0831 Å °-0.2511 Å °-0.0435 Å °0.0858 Å °0.306 Å °-0.0391 Å °-0.0843 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 141
2X-RAY DIFFRACTION1B2 - 141

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