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- PDB-2bmz: Banana Lectin bound to Xyl-b1,3 Man-a-O-Methyl (XM) -

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Basic information

Entry
Database: PDB / ID: 2bmz
TitleBanana Lectin bound to Xyl-b1,3 Man-a-O-Methyl (XM)
ComponentsRIPENING-ASSOCIATED PROTEIN
KeywordsSUGAR BINDING PROTEIN / MANNOSE-SPECIFIC JACALIN-RELATED LECTIN
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-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
: / Ripening-associated protein
Similarity search - Component
Biological speciesMUSA ACUMINATA (dwarf banana)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMeagher, J.L. / Winter, H.C. / Ezell, P. / Goldstein, I.J. / Stuckey, J.A.
CitationJournal: Glycobiology / Year: 2005
Title: Crystal Structure of Banana Lectin Reveals a Novel Second Sugar Binding Site.
Authors: Meagher, J.L. / Winter, H.C. / Ezell, P. / Goldstein, I.J. / Stuckey, J.A.
History
DepositionMar 17, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2005Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: RIPENING-ASSOCIATED PROTEIN
B: RIPENING-ASSOCIATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,06912
Polymers29,1552
Non-polymers1,91410
Water3,981221
1
A: RIPENING-ASSOCIATED PROTEIN
hetero molecules

B: RIPENING-ASSOCIATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,06912
Polymers29,1552
Non-polymers1,91410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_565x-y,-y+1,-z+1/31
Buried area2240 Å2
ΔGint-17.6 kcal/mol
Surface area15390 Å2
MethodPQS
2
B: RIPENING-ASSOCIATED PROTEIN
hetero molecules

A: RIPENING-ASSOCIATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,06912
Polymers29,1552
Non-polymers1,91410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_665x-y+1,-y+1,-z+1/31
Buried area1350 Å2
ΔGint-18.8 kcal/mol
Surface area15390 Å2
MethodPQS
Unit cell
Length a, b, c (Å)81.623, 81.623, 146.815
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 RIPENING-ASSOCIATED PROTEIN / BANANA LECTIN


Mass: 14577.413 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUSA ACUMINATA (dwarf banana) / References: UniProt: O22321
#2: Polysaccharide
beta-D-xylopyranose-(1-3)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-3DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a212h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(3+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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 Å3/Da / Density % sol: 74 %
Crystal growpH: 8.25
Details: 1.275M AMMONIUM SULFATE 30MM CADMIUM CHLORIDE 0.1M TRIS-HCL, PH=8.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.2834
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 11, 2004 / Details: MIRRORS
RadiationMonochromator: DIAMOND III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2834 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29782 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BMY

2bmy


Resolution: 2.4→9.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 479088.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2127 9.8 %RANDOM
Rwork0.228 ---
obs0.228 21764 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.4199 Å2 / ksol: 0.319993 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 110 221 2373
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 314 9.2 %
Rwork0.322 3092 -
obs--93.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4XLM.PARAMXLM.TOP

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