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- PDB-1zgr: Crystal structure of the Parkia platycephala seed lectin -

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Basic information

Entry
Database: PDB / ID: 1zgr
TitleCrystal structure of the Parkia platycephala seed lectin
ComponentsMannose/glucose-specific lectin
KeywordsSUGAR BINDING PROTEIN / beta-prism / lectin
Function / homology
Function and homology information


D-glucose binding / heterophilic cell-cell adhesion / D-mannose binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Mannose/glucose-specific lectin
Similarity search - Component
Biological speciesParkia platycephala (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGallego del Sol, F. / Cavada, B.S. / Calvete, J.J.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The first crystal structure of a mimosoideae lectin reveals a novel quaternary arrangement of a widespread domain.
Authors: Gallego Del Sol, F. / Nagano, C. / Cavada, B.S. / Calvete, J.J.
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Advisory / Data collection
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / reflns_shell
Item: _reflns_shell.Rmerge_I_obs
Revision 1.4Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannose/glucose-specific lectin
B: Mannose/glucose-specific lectin


Theoretical massNumber of molelcules
Total (without water)95,1342
Polymers95,1342
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-10 kcal/mol
Surface area35900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.597, 68.511, 208.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mannose/glucose-specific lectin


Mass: 47566.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Parkia platycephala (plant) / Tissue: seeds / References: UniProt: P83304
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.93 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→104 Å / Num. obs: 31543 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.059 / Rsym value: 0.055 / Net I/σ(I): 9.5
Reflection shellResolution: 2.002→2.11 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2060 / Rsym value: 0.101 / % possible all: 65.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.913 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.775 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24297 1555 5 %RANDOM
Rwork0.2138 ---
all0.21496 29482 --
obs0.21525 27927 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.576 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 0 169 6819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226548
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9188881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7035841
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55124.346260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58715969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.215159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025029
X-RAY DIFFRACTIONr_nbd_refined0.2180.22661
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24435
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.25
X-RAY DIFFRACTIONr_mcbond_it0.9961.54152
X-RAY DIFFRACTIONr_mcangle_it1.75626653
X-RAY DIFFRACTIONr_scbond_it2.07632396
X-RAY DIFFRACTIONr_scangle_it3.3744.52228
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 98 -
Rwork0.293 1987 -
obs-1987 88.5 %

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