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- PDB-5mb4: Crystal Structure of the Psathyrella asperospora lectin PAL in co... -

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Basic information

Entry
Database: PDB / ID: 5mb4
TitleCrystal Structure of the Psathyrella asperospora lectin PAL in complex with GlcNAc
ComponentsGlcNAc specific lectin
KeywordsSUGAR BINDING PROTEIN / Lectin / fungi / seven bladed beta propeller / GlcNAc
Function / homologyFG-GAP-like repeat / FG-GAP repeat / MALONATE ION / 2-acetamido-2-deoxy-alpha-D-glucopyranose / GlcNAc specific lectin
Function and homology information
Biological speciesPsathyrella (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRibeiro, J. / Varrot, A.
Funding support France, 1items
OrganizationGrant numberCountry
Labex ArcaneANR-11-LABX-0003-01 France
CitationJournal: Proteins / Year: 2017
Title: Biophysical characterization and structural determination of the potent cytotoxic Psathyrella asperospora lectin.
Authors: Ribeiro, J.P. / Ali Abol Hassan, M. / Rouf, R. / Tiralongo, E. / May, T.W. / Day, C.J. / Imberty, A. / Tiralongo, J. / Varrot, A.
History
DepositionNov 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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: GlcNAc specific lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,71616
Polymers42,7071
Non-polymers2,01015
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-9 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.550, 120.550, 198.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-625-

HOH

21A-681-

HOH

31A-947-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GlcNAc specific lectin


Mass: 42706.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psathyrella (fungus) / Variant: Asperospora / References: UniProt: A0A1U7Q1Z0*PLUS

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Sugars , 2 types, 8 molecules

#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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
#5: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE / N-Acetylglucosamine


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

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Non-polymers , 3 types, 354 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 3.27 Å3/Da / Density % sol: 62.35 % / Description: plate
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Protein at 10 mg per ml in PBS 2.4M sodium malonate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30.91 Å / Num. obs: 37041 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 26.3 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Net I/av σ(I): 7.5 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.608 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLM7.1.0data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2bwr

2bwr


Resolution: 2→30.91 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.643 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.139 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21449 1879 5.1 %RANDOM
Rwork0.16936 ---
obs0.17168 35162 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.193 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0.38 Å2-0 Å2
2---0.77 Å2-0 Å2
3---2.5 Å2
Refinement stepCycle: 1 / Resolution: 2→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 103 347 3466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193225
X-RAY DIFFRACTIONr_bond_other_d0.0030.022966
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9624388
X-RAY DIFFRACTIONr_angle_other_deg0.99836746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85123.958144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.115455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9471519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023726
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02789
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8432.6491610
X-RAY DIFFRACTIONr_mcbond_other1.8432.6481609
X-RAY DIFFRACTIONr_mcangle_it2.5583.9622013
X-RAY DIFFRACTIONr_mcangle_other2.5593.9632014
X-RAY DIFFRACTIONr_scbond_it2.4842.8871615
X-RAY DIFFRACTIONr_scbond_other2.4832.8861615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6284.2432375
X-RAY DIFFRACTIONr_long_range_B_refined5.11732.0333505
X-RAY DIFFRACTIONr_long_range_B_other4.92831.7643459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 131 -
Rwork0.288 2599 -
obs--99.27 %

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