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- PDB-5eyx: Monoclinic Form of Centrolobium tomentosum seed lectin (CTL) comp... -

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Basic information

Entry
Database: PDB / ID: 5eyx
TitleMonoclinic Form of Centrolobium tomentosum seed lectin (CTL) complexed with Man1-3Man-OMe.
ComponentsCentrolobium tomentosum lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Centrolobium tomentosum / Dalbergieae / Methyl Dimannoside / CTL
Function / homology
Function and homology information


D-mannose binding / toxin activity / metal ion binding
Similarity search - Function
Legume lectin / 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 ...Legume lectin / 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
: / Mannose/glucose-specific lectin
Similarity search - Component
Biological speciesCentrolobium tomentosum (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.25 Å
AuthorsAlmeida, A.C. / Osterne, V.J.S. / Santiago, M.Q. / Pinto-Junior, V.R. / Silva-Filho, J.C. / Lossio, C.F. / Almeida, R.P.H. / Teixeira, C.S. / Delatorre, P. / Rocha, B.A.M. ...Almeida, A.C. / Osterne, V.J.S. / Santiago, M.Q. / Pinto-Junior, V.R. / Silva-Filho, J.C. / Lossio, C.F. / Almeida, R.P.H. / Teixeira, C.S. / Delatorre, P. / Rocha, B.A.M. / Santiago, K.S. / Cavada, B.S.
CitationJournal: Arch.Biochem.Biophys. / Year: 2016
Title: Structural analysis of Centrolobium tomentosum seed lectin with inflammatory activity.
Authors: Almeida, A.C. / Osterne, V.J. / Santiago, M.Q. / Pinto-Junior, V.R. / Silva-Filho, J.C. / Lossio, C.F. / Nascimento, F.L. / Almeida, R.P. / Teixeira, C.S. / Leal, R.B. / Delatorre, P. / ...Authors: Almeida, A.C. / Osterne, V.J. / Santiago, M.Q. / Pinto-Junior, V.R. / Silva-Filho, J.C. / Lossio, C.F. / Nascimento, F.L. / Almeida, R.P. / Teixeira, C.S. / Leal, R.B. / Delatorre, P. / Rocha, B.A. / Assreuy, A.M. / Nascimento, K.S. / Cavada, B.S.
History
DepositionNov 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / 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_struct_oper_list / struct_asym / struct_conn / 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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrolobium tomentosum lectin
B: Centrolobium tomentosum lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,50910
Polymers54,1642
Non-polymers1,3458
Water5,567309
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-18 kcal/mol
Surface area19170 Å2
Unit cell
Length a, b, c (Å)145.840, 41.550, 94.640
Angle α, β, γ (deg.)90.000, 102.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Centrolobium tomentosum lectin


Mass: 27081.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Centrolobium tomentosum (plant) / References: UniProt: C0HJX1*PLUS

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 2
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
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 313 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Peg 8000, 2-pentanediol, Hepes sodium. / PH range: 7.0-8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.47 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.47 Å / Relative weight: 1
ReflectionResolution: 2.25→46.22 Å / Num. all: 26369 / Num. obs: 26369 / % possible obs: 98.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.56 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.055 / Rrim(I) all: 0.105 / Rsym value: 0.089 / Net I/σ(I): 10.8 / Num. measured all: 91499
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRsym value% possible all
2.25-2.373.30.4193.71213836390.8730.0260.03893.6
7.12-46.223.40.03818.530939140.9990.0280.04599.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementResolution: 2.25→35.917 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 1296 4.93 %
Rwork0.1858 25018 -
obs0.1883 26314 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.78 Å2 / Biso mean: 21.5706 Å2 / Biso min: 6.58 Å2
Refinement stepCycle: final / Resolution: 2.25→35.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3755 0 80 309 4144
Biso mean--29.22 25.57 -
Num. residues----480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123925
X-RAY DIFFRACTIONf_angle_d1.1595370
X-RAY DIFFRACTIONf_chiral_restr0.087625
X-RAY DIFFRACTIONf_plane_restr0.009694
X-RAY DIFFRACTIONf_dihedral_angle_d16.4891366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.34010.31681330.26242588272193
2.3401-2.44660.28821500.20372710286096
2.4466-2.57550.24911330.20022720285398
2.5755-2.73680.26721430.19692784292799
2.7368-2.94810.2721420.197528192961100
2.9481-3.24460.25731600.189827972957100
3.2446-3.71360.24511370.19812822295999
3.7136-4.67720.19081420.15392841298399
4.6772-35.92130.17991560.158529373093100

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