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- PDB-3qlq: Crystal structure of Concanavalin A bound to an octa-alpha-mannos... -

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Basic information

Entry
Database: PDB / ID: 3qlq
TitleCrystal structure of Concanavalin A bound to an octa-alpha-mannosyl-octasilsesquioxane cluster
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / Concanavalin A-like lectins/glucanases / Sugar Binding
Function / homology
Function and homology information


D-mannose binding / metal ion binding
Similarity search - Function
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
alpha-D-mannopyranose / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia cathartica (xiao dao dou)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSundberg, E.J. / Bonsor, D.A. / Trastoy, B. / Chiara, J.L.
CitationJournal: Adv Funct Mater / Year: 2012
Title: Synthesis and Biophysical Study of Disassembling Nano hybrid Bioconjugates with a Cubic Octasilsesquioxane Core
Authors: Trastoy, B. / Bonsor, D.A. / Perez-Ojeda, M.E. / Sundberg, E.J. / Jimeno, M.L. / Garcia-Fernandez, J.M. / Chiara, J.L.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 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

Downloads & links

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Assembly

Deposited unit
A: Concanavalin-A
B: Concanavalin-A
C: Concanavalin-A
D: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,59016
Polymers102,4904
Non-polymers1,10112
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-103 kcal/mol
Surface area33140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.890, 63.680, 125.800
Angle α, β, γ (deg.)90.00, 93.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Canavalia cathartica (xiao dao dou) / References: UniProt: P81461
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% PEG 2K MME, 1mM Manganese Chloride, 1mM Calcium Chloride, 100mM HEPES pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 5, 2010 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→31.84 Å / Num. all: 104059 / Num. obs: 100001 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 13.9
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.3 / % possible all: 88

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Processing

Software
NameVersionClassification
Blu-IceICE/DCSdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SCR

1scr


Resolution: 1.7→31.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.378 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24832 4961 5 %RANDOM
Rwork0.21783 ---
all0.21942 98996 --
obs0.21942 94987 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.338 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20.01 Å2
2--3.12 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7111 0 56 253 7420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0227374
X-RAY DIFFRACTIONr_bond_other_d0.0010.024753
X-RAY DIFFRACTIONr_angle_refined_deg1.9861.9510072
X-RAY DIFFRACTIONr_angle_other_deg1.04311680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7035947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0324.836304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.351151127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.611524
X-RAY DIFFRACTIONr_chiral_restr0.1160.21177
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021446
X-RAY DIFFRACTIONr_mcbond_it1.3121.54698
X-RAY DIFFRACTIONr_mcbond_other0.381.51903
X-RAY DIFFRACTIONr_mcangle_it2.20627598
X-RAY DIFFRACTIONr_scbond_it2.94232676
X-RAY DIFFRACTIONr_scangle_it4.4174.52467
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 322 -
Rwork0.346 6325 -
obs--86.96 %

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