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- PDB-4i30: Crystal structure of Canavalia maritima seeds lectin (ConM) co-cr... -

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Basic information

Entry
Database: PDB / ID: 4i30
TitleCrystal structure of Canavalia maritima seeds lectin (ConM) co-crystalized with gamma-aminobutyric acid (GABA) and soaked with adenine
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / Beta-sandwich / jelly-roll / Sugar-binding protein
Function / homology
Function and homology information


D-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
GAMMA-AMINO-BUTANOIC ACID / ADENINE / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia lineata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsDelatorre, P. / Silva-Filho, J.C. / Nobrega, R.B. / Gadelha, C.A.A. / Cavada, B.S. / Rocha, B.A.M. / Santi-Gadelha, T. / Teixeira, C.S.
CitationJournal: To be Published
Title: Crystal structure of Canavalia maritima seeds lectin (ConM) co-crystalized with gamma-aminobutyric acid (GABA) and soaked with adenine
Authors: Delatorre, P. / Silva-Filho, J.C. / Nobrega, R.B. / Gadelha, C.A.A. / Cavada, B.S. / Rocha, B.A.M. / Santi-Gadelha, T. / Teixeira, C.S.
History
DepositionNov 23, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionDec 12, 2012ID: 3S0S
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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 / _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: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8275
Polymers25,4941
Non-polymers3334
Water1,56787
1
A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules

A: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,31020
Polymers101,9774
Non-polymers1,33316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area9110 Å2
ΔGint-114 kcal/mol
Surface area31880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.990, 70.410, 97.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Concanavalin-A / Con A


Mass: 25494.195 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canavalia lineata (plant) / References: UniProt: P81460

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Non-polymers , 5 types, 91 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM
#5: Chemical ChemComp-ADE / ADENINE / Adenine


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS INDICATE THAT THE RESIDUE AT THIS POSITION SHOULD BE AS INDICATED IN SEQRES.

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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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0 M Ammonium sulphate, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 5, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.427 Å / Relative weight: 1
ReflectionResolution: 1.89→57 Å / Num. all: 17782 / Num. obs: 16822 / % possible obs: 99.78 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 5.7
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.366 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
REFMAC5.5.0110refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→57 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.929 / SU B: 8.887 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26413 960 5.1 %RANDOM
Rwork0.22227 ---
all0.2259 17782 --
obs0.22438 16822 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---6.89 Å20 Å2
3---6.49 Å2
Refinement stepCycle: LAST / Resolution: 1.89→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 19 87 1867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221811
X-RAY DIFFRACTIONr_angle_refined_deg2.5771.9512465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9715229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31724.7374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.55515279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.112156
X-RAY DIFFRACTIONr_chiral_restr0.1740.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211371
X-RAY DIFFRACTIONr_mcbond_it2.0861.51148
X-RAY DIFFRACTIONr_mcangle_it3.07521856
X-RAY DIFFRACTIONr_scbond_it4.5193663
X-RAY DIFFRACTIONr_scangle_it6.1134.5609
X-RAY DIFFRACTIONr_rigid_bond_restr2.7431811
X-RAY DIFFRACTIONr_sphericity_free14.294389
X-RAY DIFFRACTIONr_sphericity_bonded9.91631772
LS refinement shellResolution: 1.889→1.938 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 67 -
Rwork0.286 1269 -
obs--98.74 %

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