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- PDB-4k21: Crystal structure of Canavalia boliviana lectin in complex with Xman -

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Basic information

Entry
Database: PDB / ID: 4k21
TitleCrystal structure of Canavalia boliviana lectin in complex with Xman
ComponentsCanavalia boliviana lectin
KeywordsMannose Binding Protein / Diocleinae lectins / Dimannosides / Oligomerization / Binding Sites / Jelly roll / Carbohydrate binding
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
: / Chem-XMM / Lectin alpha chain
Similarity search - Component
Biological speciesCanavalia boliviana (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsBezerra, G.A. / Moura, T.R. / Viertlmayr, R. / Delatorre, P. / Rocha, B.A.M. / Nagano, C.S. / Gruber, K. / Cavada, B.S.
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 1.2Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 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

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Assembly

Deposited unit
A: Canavalia boliviana lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1004
Polymers25,5961
Non-polymers5043
Water3,369187
1
A: Canavalia boliviana lectin
hetero molecules

A: Canavalia boliviana lectin
hetero molecules

A: Canavalia boliviana lectin
hetero molecules

A: Canavalia boliviana lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,40016
Polymers102,3864
Non-polymers2,01512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area11620 Å2
ΔGint-117 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.970, 66.590, 108.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Canavalia boliviana lectin


Mass: 25596.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Seeds / Source: (natural) Canavalia boliviana (plant) / References: UniProt: A0A023GPI8*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-XMM / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside / (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL / (5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE / 5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl D-mannoside / 5-bromo-4-chloro-1H-indol-3-yl mannoside


Type: D-saccharide / Mass: 408.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H15BrClNO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 293 K / Method: vapor difusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 3 M sodium formate, vapor difusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4558 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4558 Å / Relative weight: 1
ReflectionResolution: 1.6→56.792 Å / Num. all: 29896 / Num. obs: 29896 / % possible obs: 95.1 % / Observed criterion σ(I): 3.7 / Redundancy: 6.4 % / Rsym value: 0.068 / Net I/σ(I): 17.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.20.2073.71050532650.20773
1.69-1.7950.1742025940750.1794.9
1.79-1.9170.1235.22801339950.12399.5
1.91-2.0770.0817.12654337700.08199.8
2.07-2.267.10.0767.52468134760.076100
2.26-2.537.10.0678.72266031770.067100
2.53-2.927.20.0628.92014628140.062100
2.92-3.587.20.0727.71728724020.072100
3.58-5.067.10.0629.31326118660.06299.4
5.06-28.3966.70.05211707310560.05297.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.81 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.4 Å
Translation2.5 Å28.4 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→28.396 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.8853 / SU ML: 0.18 / σ(F): 0 / Phase error: 18.3 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1916 1499 5.06 %
Rwork0.1462 --
obs0.1485 29896 91 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.799 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso max: 72.82 Å2 / Biso mean: 23.2175 Å2 / Biso min: 11.66 Å2
Baniso -1Baniso -2Baniso -3
1--4.2153 Å20 Å20 Å2
2--0.8338 Å2-0 Å2
3---3.3815 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 25 187 2019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011954
X-RAY DIFFRACTIONf_angle_d1.3142689
X-RAY DIFFRACTIONf_chiral_restr0.086310
X-RAY DIFFRACTIONf_plane_restr0.006344
X-RAY DIFFRACTIONf_dihedral_angle_d12.158727
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62760.2268590.18781440149950
1.6276-1.65720.2617970.17161679177659
1.6572-1.68910.2181210.15991939206069
1.6891-1.72350.21200.14862215233578
1.7235-1.7610.20461230.13272614273790
1.761-1.8020.20721450.12422688283394
1.802-1.8470.14851690.11592691286095
1.847-1.8970.18681470.12562752289997
1.897-1.95280.17141520.11562749290198
1.9528-2.01580.13851410.11832815295698
2.0158-2.08780.15131640.13842834299899
2.0878-2.17140.1921350.13382867300299
2.1714-2.27010.19031250.1272829295499
2.2701-2.38980.18421590.12812860301999
2.3898-2.53940.22871320.157528442976100
2.5394-2.73530.21391750.166128273002100
2.7353-3.01030.19921590.16128302989100
3.0103-3.44530.18731330.151428843017100
3.4453-4.33820.17721580.139528412999100
4.3382-28.3960.21361570.17172796295398

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