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- PDB-4xtp: Crystal structure of a recombinant Vatairea macrocarpa seed lecti... -

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Basic information

Entry
Database: PDB / ID: 4xtp
TitleCrystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with Tn antigen
ComponentsSeed lectin
KeywordsSUGAR BINDING PROTEIN / legume / recombinant lectin / vatairea / Tn antigen
Function / homology
Function and homology information


carbohydrate binding / 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
2-acetamido-2-deoxy-alpha-D-galactopyranose / CITRIC ACID / : / SERINE / Seed lectin
Similarity search - Component
Biological speciesVatairea macrocarpa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSousa, B.L. / Silva-Filho, J.C. / Kumar, P. / Lyskowski, A. / Bezerra, G.A. / Delatorre, P. / Rocha, B.A.M. / Cunha, R.M.S. / Nagano, C.S. / Gruber, K. / Cavada, B.S.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2016
Title: Crystal structure of a recombinant Vatairea macrocarpa seed lectin
Authors: Sousa, B.L. / Silva-Filho, J.C. / Kumar, P. / Lyskowski, A. / Bezerra, G.A. / Delatorre, P. / Rocha, B.A.M. / Cunha, R.M.S. / Nagano, C.S. / Gruber, K. / Cavada, B.S.
History
DepositionJan 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / 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_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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,78113
Polymers27,4951
Non-polymers1,28612
Water2,432135
1
A: Seed lectin
hetero molecules

A: Seed lectin
hetero molecules

A: Seed lectin
hetero molecules

A: Seed lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,12552
Polymers109,9824
Non-polymers5,14448
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 area13180 Å2
ΔGint-427 kcal/mol
Surface area34440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.093, 86.024, 128.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Seed lectin / VML


Mass: 27495.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vatairea macrocarpa (plant) / Organ: Seed / Plasmid: pET-28a / Details (production host): C-terminal histag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P81371
#7: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 146 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.04 Å3/Da / Density % sol: 59.48 % / Description: Cubic-like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: Cubic-like crystals / PH range: 3.0 - 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 1.968→71.55 Å / Num. obs: 22033 / % possible obs: 97.7 % / Redundancy: 6.2 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.122 / Rsym value: 0.112 / Net I/av σ(I): 5.276 / Net I/σ(I): 10 / Num. measured all: 136723
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.97-2.075.80.5211.31594227620.2290.5212.885.3
2.07-2.26.70.5371.22042930670.2280.5373.5100
2.2-2.3560.4611.41739228890.2120.461499.7
2.35-2.546.10.242.91653026920.1060.246.199.9
2.54-2.786.70.183.91678524940.0750.188.6100
2.78-3.116.60.1225.71494822630.0520.12212.4100
3.11-3.595.90.0887.81183720180.040.08816.899.8
3.59-4.45.70.0659.6974917030.030.06521.999.5
4.4-6.226.30.04911.3846713480.0210.04924.999.8
6.22-46.9865.80.03615.346447970.0160.03624.199.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
Cootmodel building
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U2A

4u2a


Resolution: 1.97→71.55 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2387 / WRfactor Rwork: 0.1857 / FOM work R set: 0.7857 / SU B: 10.048 / SU ML: 0.123 / SU R Cruickshank DPI: 0.3771 / SU Rfree: 0.1619 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.377 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 1123 5.2 %RANDOM
Rwork0.1979 ---
obs0.2007 20674 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.26 Å2 / Biso mean: 29.233 Å2 / Biso min: 17.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å20 Å2
2--2.67 Å20 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 1.97→71.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 71 135 2017
Biso mean--37.61 32.75 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021945
X-RAY DIFFRACTIONr_bond_other_d0.0010.021752
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9692659
X-RAY DIFFRACTIONr_angle_other_deg2.35934057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2545239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16524.93881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04115296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.997155
X-RAY DIFFRACTIONr_chiral_restr0.0880.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212166
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02431
X-RAY DIFFRACTIONr_mcbond_it2.6942.778947
X-RAY DIFFRACTIONr_mcbond_other2.6682.771943
X-RAY DIFFRACTIONr_mcangle_it2.6144.1581183
X-RAY DIFFRACTIONr_rigid_bond_restr4.98933697
X-RAY DIFFRACTIONr_sphericity_free9.363539
X-RAY DIFFRACTIONr_sphericity_bonded4.74853754
LS refinement shellResolution: 1.968→2.019 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 64 -
Rwork0.262 1108 -
all-1172 -
obs--71.55 %

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