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- PDB-4k1y: Crystal structure of Canavalia boliviana lectin in complex with M... -

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Basic information

Entry
Database: PDB / ID: 4k1y
TitleCrystal structure of Canavalia boliviana lectin in complex with Man1-3Man-OMe
ComponentsCanavalia boliviana lectin
KeywordsMannose Binding Protein / Diocleinae lectins / Dimannosides / Oligomerization / Binding Sites
Function / homology
Function and homology information


mannose binding / metal ion binding
Similarity search - Function
Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Lectin alpha chain
Similarity search - Component
Biological speciesCanavalia boliviana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsBezerra, G.A. / Viertlmayr, R. / Moura, T.R. / Delatorre, P. / Rocha, B.A.M. / Cavada, B.S. / Gruber, K.
CitationJournal: Plos One / Year: 2014
Title: Structural Studies of an Anti-Inflammatory Lectin from Canavalia boliviana Seeds in Complex with Dimannosides.
Authors: Bezerra, G.A. / Viertlmayr, R. / Moura, T.R. / Delatorre, P. / Rocha, B.A. / do Nascimento, K.S. / Figueiredo, J.G. / Bezerra, I.G. / Teixeira, C.S. / Simoes, R.C. / Nagano, C.S. / de ...Authors: Bezerra, G.A. / Viertlmayr, R. / Moura, T.R. / Delatorre, P. / Rocha, B.A. / do Nascimento, K.S. / Figueiredo, J.G. / Bezerra, I.G. / Teixeira, C.S. / Simoes, R.C. / Nagano, C.S. / de Alencar, N.M. / Gruber, K. / Cavada, B.S.
History
DepositionApr 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
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_conn_angle / pdbx_validate_close_contact / 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.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Canavalia boliviana lectin
B: Canavalia boliviana lectin
C: Canavalia boliviana lectin
D: Canavalia boliviana lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,20325
Polymers102,3864
Non-polymers2,81721
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12550 Å2
ΔGint-170 kcal/mol
Surface area32540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.880, 95.660, 94.610
Angle α, β, γ (deg.)90.000, 132.290, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Canavalia boliviana lectin


Mass: 25596.377 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Seeds / Source: (natural) Canavalia boliviana (plant) / References: UniProt: A0A023GPI8*PLUS
#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5_1*OC][a1122h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 205 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cd
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 293 K / Method: vapor difusion, hanging drop / pH: 4.6
Details: 0.1 M CdCl2, 0.1M NaOAc, 30% PEG 400, pH 4.6, vapor difusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 2, 2010 / Details: mirrors
RadiationMonochromator: BARTELS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
Reflection twinOperator: -h-2*l,-k,l / Fraction: 0.296
ReflectionResolution: 2.5→70.243 Å / Num. all: 31961 / Num. obs: 31961 / % possible obs: 99.9 % / Observed criterion σ(I): 1.1 / Redundancy: 5.6 % / Rsym value: 0.139 / Net I/σ(I): 9.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.645.60.6781.12587746240.678100
2.64-2.85.60.4841.62466343940.484100
2.8-2.995.60.3222.42327141380.322100
2.99-3.235.60.23.92168338530.2100
3.23-3.545.60.1425.32024135970.142100
3.54-3.955.30.1384.11694931690.13899.5
3.95-4.565.60.0759.81607828510.075100
4.56-5.595.60.0719.91353424130.071100
5.59-7.915.60.06810.11050518780.068100
7.91-40.9445.40.04513.9564410440.04599.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.09 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.94 Å
Translation2.5 Å40.94 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.944 Å / Occupancy max: 1 / Occupancy min: 0.57 / FOM work R set: 0.7493 / σ(F): 0 / Phase error: 32.21 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2281 1621 5.07 %
Rwork0.2037 --
all0.2045 --
obs0.2045 31961 99.94 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.15 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 86.04 Å2 / Biso mean: 32.0985 Å2 / Biso min: 12.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.5753 Å20 Å28.2955 Å2
2---1.0745 Å20 Å2
3---1.6498 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7228 0 113 188 7529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097745
X-RAY DIFFRACTIONf_angle_d1.03210212
X-RAY DIFFRACTIONf_chiral_restr0.0721192
X-RAY DIFFRACTIONf_plane_restr0.0031300
X-RAY DIFFRACTIONf_dihedral_angle_d10.9992664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.57360.32721460.30022498264494
2.5736-2.65660.36691280.27932531265995
2.6566-2.75150.26611310.25932504263595
2.7515-2.86160.26961290.24582507263695
2.8616-2.99170.28161260.22432536266295
2.9917-3.14930.22281310.2022536266795
3.1493-3.34650.2141360.19362505264195
3.3465-3.60450.21351500.18992520267094
3.6045-3.96670.30871380.27282508264694
3.9667-4.53940.17481370.14652544268195
4.5394-5.7140.15771470.13832530267795
5.714-32.44990.18691150.18152619273496

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