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- PDB-5byn: Canavalia maritima lectin complexed with synthetic selenoamino acid -

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Basic information

Entry
Database: PDB / ID: 5byn
TitleCanavalia maritima lectin complexed with synthetic selenoamino acid
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / Lectin / seleno amiinoacid
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
Chem-4WM / : / : / DI(HYDROXYETHYL)ETHER / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia lineata (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsNobrega, R.B. / Silva-Filho, J.C. / Kawasoko, C.Y. / Rodrigues, O.E.D. / Schwab, R.S. / Braga, A.L. / Delatorre, P. / Cavada, B.S.
CitationJournal: To Be Published
Title: Canavalia maritima lectin complexed with synthetic selenoamino acid
Authors: Nobrega, R.B. / Silva-Filho, J.C. / Kawasoko, C.Y. / Rodrigues, O.E.D. / Schwab, R.S. / Braga, A.L. / Delatorre, P. / Cavada, B.S.
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Concanavalin-A
B: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,39813
Polymers51,0422
Non-polymers1,35611
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-41 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.640, 190.640, 190.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Concanavalin-A / Con A


Mass: 25521.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canavalia lineata (plant) / References: UniProt: P81460

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Non-polymers , 7 types, 76 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-4WM / (4R)-4-{[(S)-tert-butoxy(hydroxy)methyl]amino}-5-[(1S)-cyclohex-2-en-1-ylselanyl]pentane-1,1-diol


Mass: 380.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H31NO4Se
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Hepes-Na, ammonium sulfate, PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.42 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.42 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.912
11-H, L, K20.088
ReflectionResolution: 2.651→110.066 Å / Num. all: 16760 / Num. obs: 16760 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rpim(I) all: 0.048 / Rrim(I) all: 0.126 / Rsym value: 0.117 / Net I/av σ(I): 3.497 / Net I/σ(I): 9.8 / Num. measured all: 110321
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.65-2.795.60.33621358424310.1530.3363.999.9
2.79-2.966.10.2562.41375222670.1130.2565.4100
2.96-3.176.50.1833.21424021800.0770.1837.6100
3.17-3.426.90.1413.41389420240.0580.1419.8100
3.42-3.7570.1134.51299818610.0460.11311.7100
3.75-4.1970.1024.81191516920.0410.10213100
4.19-4.8470.1074.71049414900.0430.10714.6100
4.84-5.9370.1114.5888112680.0440.11114.4100
5.93-8.3870.0945.169749970.0380.09414.2100
8.38-38.9146.50.0944.435895500.0410.09414.597

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.651→38.91 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.2988 / WRfactor Rwork: 0.2196 / FOM work R set: 0.7795 / SU B: 23.033 / SU ML: 0.223 / SU R Cruickshank DPI: 0.0624 / SU Rfree: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2779 858 5.1 %RANDOM
Rwork0.2039 ---
obs0.2075 15900 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.58 Å2 / Biso mean: 42.582 Å2 / Biso min: 26.96 Å2
Baniso -1Baniso -2Baniso -3
1--7.75 Å218.28 Å2-4.62 Å2
2--21.51 Å2-7.69 Å2
3----13.76 Å2
Refinement stepCycle: final / Resolution: 2.651→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 0 68 65 3722
Biso mean--39.35 33.48 -
Num. residues----472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193744
X-RAY DIFFRACTIONr_bond_other_d0.0010.023482
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.9515092
X-RAY DIFFRACTIONr_angle_other_deg2.29438030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.795471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.224.808156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88715570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4341512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214234
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02844
X-RAY DIFFRACTIONr_mcbond_it1.1752.5561891
X-RAY DIFFRACTIONr_mcbond_other1.1752.5561890
X-RAY DIFFRACTIONr_mcangle_it1.5643.8392358
X-RAY DIFFRACTIONr_rigid_bond_restr2.45337221
X-RAY DIFFRACTIONr_sphericity_free7.031527
X-RAY DIFFRACTIONr_sphericity_bonded2.46257194
LS refinement shellResolution: 2.651→2.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 55 -
Rwork0.279 1194 -
all-1249 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.299-0.3404-1.22571.95840.0023.04540.16390.27510.2306-0.0660.00620.0355-0.224-0.3074-0.17020.14390.01690.07350.04750.03060.058149.93513.51430.312
22.71270.234-0.63591.8693-0.32813.4106-0.176-0.2523-0.2932-0.02930.0183-0.12680.2520.2720.15760.06030.03250.07220.03930.03310.103264.753-13.4745.317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 237
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION1B301
4X-RAY DIFFRACTION2B1 - 237
5X-RAY DIFFRACTION2A306
6X-RAY DIFFRACTION2B302 - 303

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