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- PDB-2gme: Metal-free (apo) P. angolensis seed lectin -

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Basic information

Entry
Database: PDB / ID: 2gme
TitleMetal-free (apo) P. angolensis seed lectin
Componentslectin
KeywordsSUGAR BINDING PROTEIN / legume lectin / metal-free lectin / beta sandwich
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 ...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
Biological speciesPterocarpus angolensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGarcia-Pino, A. / Buts, L. / Wyns, L. / Loris, R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Interplay Between Metal Binding and cis/trans Isomerization in Legume Lectins: Structural and Thermodynamic Study of P. angolensis Lectin.
Authors: Garcia-Pino, A. / Buts, L. / Wyns, L. / Loris, R.
History
DepositionApr 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: lectin
B: lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3094
Polymers55,1172
Non-polymers1922
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-36 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.883, 62.000, 130.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsSubunits A and B together form the lectin dimer

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Components

#1: Protein lectin


Mass: 27558.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pterocarpus angolensis (plant) / Tissue: seed / References: UniProt: Q8GSD2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 10% PEG 6000, 20% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.75→15 Å / Num. all: 48243 / Num. obs: 48243 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.75→1.81 Å / % possible all: 93.3

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
PHASERphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1UKG

1ukg


Resolution: 1.75→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 3859 RANDOM
Rwork0.193 --
all0.195 48243 -
obs0.195 48243 -
Refinement stepCycle: LAST / Resolution: 1.75→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 10 348 3879
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.51

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