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- PDB-1qgl: Room temperature structure of concanavalin A complexed to bivalen... -

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Basic information

Entry
Database: PDB / ID: 1qgl
TitleRoom temperature structure of concanavalin A complexed to bivalent ligand
ComponentsPROTEIN (SUCCINYLATED CONCANAVALIN A )
KeywordsLECTIN (AGGLUTININ) / CONCANAVLIN A / SACCHARIDE BINDING / RECOGNITION COMPLEX
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / 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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / 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 domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-EJT / : / SUCCINIC ACID / Concanavalin-A / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsNaismith, J.H.
CitationJournal: J.Am.Chem.Soc. / Year: 1999
Title: On the Meaning of Affinity: Cluster Glycoside Effects and Concanavalin A
Authors: Dimick, S.M. / Powell, S.C. / Mcmahon, S.A. / Moothoo, D.N. / Naismith, J.H. / Toone, E.J.
History
DepositionApr 30, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.source
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (SUCCINYLATED CONCANAVALIN A )
B: PROTEIN (SUCCINYLATED CONCANAVALIN A )
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2138
Polymers51,2452
Non-polymers9686
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.100, 127.400, 118.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.68145, -0.00034, 0.73186), (0.00281, 0.99999, 0.00308), (-0.73186, 0.00416, -0.68144)
Vector: -31.51094, 0.05166, 126.65054)

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein PROTEIN (SUCCINYLATED CONCANAVALIN A ) / CON A


Mass: 25622.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: COMPLEXED WITH BIVALENT LIGAND / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P81461, UniProt: P02866*PLUS
#4: Sugar ChemComp-EJT / 1,3-DI(N-PROPYLOXY-A-MANNOPYRANOSYL)-CARBOMYL 5-METHYAZIDO-BENZENE


Type: saccharide / Mass: 659.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H41N5O14

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Non-polymers , 4 types, 77 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.66 Å3/Da / Density % sol: 66.41 %
Crystal growpH: 6 / Details: pH 6
Crystal
*PLUS
Density % sol: 65 %
Crystal grow
*PLUS
Temperature: 293.5 K / pH: 7 / Method: vapor diffusion, sitting drop / Details: Moothoo, D.N., (1998) Acta Crystallogr, D54, 1023.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 mMprotein1drop
218 mMligand1drop
320 mMTris1drop
4100 mM1dropNaCl
51 mM1dropCaCl2
61 mM1dropMnCl2
720 %PEG60001reservoir
8100 mMcitric acid1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: NONIUS / Detector: IMAGE PLATE / Details: MIRROR
RadiationMonochromator: NI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.66→26 Å / Num. obs: 21164 / % possible obs: 96.8 % / Redundancy: 2.5 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072
Reflection
*PLUS
Lowest resolution: 26 Å / Num. obs: 21182 / % possible obs: 96.4 %
Reflection shell
*PLUS
Highest resolution: 2.66 Å / Lowest resolution: 2.75 Å / % possible obs: 98.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.207

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CNA

5cna


Resolution: 2.66→26 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2919789.43 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2143 10.1 %RANDOM
Rwork0.176 ---
obs-21164 96.8 %-
Solvent computationSolvent model: CNS DEFAULT
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.66 Å20 Å20 Å2
2--1.35 Å20 Å2
3---4.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.66→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3618 0 57 72 3747
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it3.022.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.66→2.83 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 284 9.3 %
Rwork0.224 2770 -
obs--84.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CONA.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMEJT.TOP
Software
*PLUS
Name: CNS / Version: 0.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 26 Å / % reflection Rfree: 10 % / Rfactor obs: 0.176 / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
X-RAY DIFFRACTIONc_angle_deg1.7
LS refinement shell
*PLUS
Rfactor Rfree: 0.257 / Rfactor obs: 0.239

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