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- PDB-2c4d: 2.6A Crystal Structure of Psathyrella velutina Lectin in Complex ... -

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Basic information

Entry
Database: PDB / ID: 2c4d
Title2.6A Crystal Structure of Psathyrella velutina Lectin in Complex with N-acetylglucosamine
ComponentsPSATHYRELLA VELUTINA LECTIN PVL
KeywordsLECTIN / PSATHYRELLA VELUTINA / N-ACETYLGLUCOSAMINE
Function / homologyFG-GAP-like repeat / FG-GAP repeat / Integrin alpha, N-terminal / metal ion binding / Lectin PVL
Function and homology information
Biological speciesPSATHYRELLA VELUTINA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCioci, G. / Mitchell, E.P. / Chazalet, V. / Gautier, C. / Oscarson, S. / Debray, H. / Perez, S. / Imberty, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Beta-Propeller Crystal Structure of Psathyrella Velutina Lectin: An Integrin-Like Fungal Protein Interacting with Monosaccharides and Calcium.
Authors: Cioci, G. / Mitchell, E.P. / Chazalet, V. / Debray, H. / Oscarson, S. / Lahmann, M. / Gautier, C. / Breton, C. / Perez, S. / Imberty, A.
History
DepositionOct 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 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

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Assembly

Deposited unit
A: PSATHYRELLA VELUTINA LECTIN PVL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,76912
Polymers43,0171
Non-polymers1,75211
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.767, 106.767, 86.622
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PSATHYRELLA VELUTINA LECTIN PVL


Mass: 43017.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: WILD MUSHROOM / Source: (natural) PSATHYRELLA VELUTINA (fungus) / References: UniProt: Q309D1*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS SEQUENCE NOT YET DEPOSITED IN SEQUENCE DATABASE. RESIDUE THR 3 HAS BEEN MUTATED TO VAL 3. ...AUTHORS SEQUENCE NOT YET DEPOSITED IN SEQUENCE DATABASE. RESIDUE THR 3 HAS BEEN MUTATED TO VAL 3. THE GENBANK REFERENCE CODE FOR THIS ENTRY IS GQ232759.

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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: 3.3 Å3/Da / Density % sol: 62.6 %
Crystal growpH: 6.5 / Details: 2.2M AMMONIUM SULPHATE 0.1M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.953
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 14, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.5→25.64 Å / Num. obs: 17901 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 11.13 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.47
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 11.29 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.57 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BWM

2bwm


Resolution: 2.6→92.45 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.161 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.47 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 912 5.1 %RANDOM
Rwork0.202 ---
obs0.205 16965 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.7 Å20 Å2
2--1.39 Å20 Å2
3----2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.6→92.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 111 55 3204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223211
X-RAY DIFFRACTIONr_bond_other_d0.0010.022848
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9594365
X-RAY DIFFRACTIONr_angle_other_deg0.84136548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7855400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.34123.878147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56715465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8741521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02684
X-RAY DIFFRACTIONr_nbd_refined0.1980.2584
X-RAY DIFFRACTIONr_nbd_other0.1980.23025
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21541
X-RAY DIFFRACTIONr_nbtor_other0.0870.21935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7121.51999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2323117
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.71831387
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6274.51248
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 63
Rwork0.32 1226

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