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- PDB-5eyy: Tetragonal Form of Centrolobium tomentosum seed lectin (CTL) comp... -

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Basic information

Entry
Database: PDB / ID: 5eyy
TitleTetragonal Form of Centrolobium tomentosum seed lectin (CTL) complexed with Man1-3Man-OMe.
ComponentsCentrolobium tomentosum lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / Centrolobium tomentosum / Dalbergieae / CTL / Methyl Dimannoside.
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: 1.902 Å
AuthorsPinto-Junior, V.R. / Osterne, V.J.S. / Santiago, M.Q. / Almeida, A.C. / Lossio, C.F. / Silva-Filho, J.C. / Almeida, R.P.H. / Teixeira, C.S. / Delatorre, P. / Rocha, B.A.M. ...Pinto-Junior, V.R. / Osterne, V.J.S. / Santiago, M.Q. / Almeida, A.C. / Lossio, C.F. / Silva-Filho, J.C. / Almeida, R.P.H. / Teixeira, C.S. / Delatorre, P. / Rocha, B.A.M. / Nascimento, 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_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.ptnr2_label_asym_id / _pdbx_struct_oper_list.symmetry_operation
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7545
Polymers27,0821
Non-polymers6734
Water4,071226
1
A: Centrolobium tomentosum lectin
hetero molecules

A: Centrolobium tomentosum lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,50910
Polymers54,1642
Non-polymers1,3458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3570 Å2
ΔGint-32 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.580, 72.580, 128.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-542-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Centrolobium tomentosum lectin


Mass: 27081.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Centrolobium tomentosum (plant) / References: UniProt: C0HJX1*PLUS

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 356.323 Da / Num. of mol.: 1
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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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, 228 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / 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: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.47 Å / Relative weight: 1
ReflectionResolution: 1.902→63.19 Å / Num. all: 27589 / Num. obs: 27589 / % possible obs: 99 % / Redundancy: 8 % / Biso Wilson estimate: 16.41 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.072 / Rsym value: 0.067 / Net I/av σ(I): 7.666 / Net I/σ(I): 19.1 / Num. measured all: 219670
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
1.9-27.80.1653.62907637350.0630.16510.294.3
2-2.127.90.1394.42998237870.0530.13913.2100
2.12-2.277.80.1175.22762335580.0440.11715.4100
2.27-2.457.70.1025.82551633220.0380.10216.5100
2.45-2.697.70.0748.22384130850.0280.07418.1100
2.69-37.90.06392199027990.0250.06321.2100
3-3.478.10.05410.62021524890.020.05427100
3.47-4.258.80.05410.61874421410.0190.05432.1100
4.25-6.018.90.04512.71501616960.0160.04532.2100
6.01-32.4597.80.03816.676679770.0140.0382596.3

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementResolution: 1.902→32.459 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1772 1350 4.91 %
Rwork0.1556 26144 -
obs0.1566 27494 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 48.96 Å2 / Biso mean: 17.1236 Å2 / Biso min: 8.66 Å2
Refinement stepCycle: final / Resolution: 1.902→32.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 40 226 2132
Biso mean--22.76 25.22 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091963
X-RAY DIFFRACTIONf_angle_d0.8862668
X-RAY DIFFRACTIONf_chiral_restr0.061312
X-RAY DIFFRACTIONf_plane_restr0.005345
X-RAY DIFFRACTIONf_dihedral_angle_d11.9581129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9024-1.97030.23041280.16372430X-RAY DIFFRACTION94
1.9703-2.04920.17481270.14762593X-RAY DIFFRACTION100
2.0492-2.14250.21521370.15692581X-RAY DIFFRACTION100
2.1425-2.25540.17911310.14912575X-RAY DIFFRACTION100
2.2554-2.39670.17221430.14612574X-RAY DIFFRACTION100
2.3967-2.58160.16971420.15592636X-RAY DIFFRACTION100
2.5816-2.84130.17531330.15842611X-RAY DIFFRACTION100
2.8413-3.25210.20871310.16612637X-RAY DIFFRACTION100
3.2521-4.0960.14991300.15852704X-RAY DIFFRACTION100
4.096-32.46350.16741480.15042803X-RAY DIFFRACTION99

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