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- PDB-1bxh: CONCANAVALIN A COMPLEXED TO METHYL ALPHA1-2 MANNOBIOSIDE -

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Basic information

Entry
Database: PDB / ID: 1bxh
TitleCONCANAVALIN A COMPLEXED TO METHYL ALPHA1-2 MANNOBIOSIDE
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE CONFORMATION / CON A SACCHARIDE COMPLEX / MOLECULAR RECOGNITION / THERMODYNAMICS
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, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / 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
methyl alpha-D-mannopyranoside / : / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMoothoo, D.N. / Canaan, B. / Field, R.A. / Naismith, J.H.
Citation
Journal: Glycobiology / Year: 1999
Title: Man alpha1-2 Man alpha-OMe-concanavalin A complex reveals a balance of forces involved in carbohydrate recognition.
Authors: Moothoo, D.N. / Canan, B. / Field, R.A. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: A General Method for Co-Crystallisation of Concanavalin a with Carbohydrates
Authors: Moothoo, D.N. / Naismith, J.H.
#2: Journal: Glycobiology / Year: 1998
Title: Concanavalin a Distorts the B-Glcnac-(1-2)-Man Linkage of B-Glcnac-(1-2)-A-Man- (1-3)-[B-Glcnac-(1-2)-A-Man-(1-6)]-Man Upon Binding,
Authors: Moothoo, D.N. / Naismith, J.H.
History
DepositionOct 2, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Advisory / Database references ...Advisory / Database references / Refinement description / Source and taxonomy / Structure summary
Category: database_PDB_caveat / entity ...database_PDB_caveat / entity / entity_name_com / entity_src_nat / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _struct_ref_seq.ref_id
Revision 1.4Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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)103,99916
Polymers102,4904
Non-polymers1,50912
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11710 Å2
ΔGint-107 kcal/mol
Surface area32740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.700, 119.700, 68.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.997798, 0.008762, -0.065744), (0.003385, -0.983214, -0.182423), (-0.066238, -0.182244, 0.98102)36.9761, 67.124, 7.4534
2given(0.789948, -0.613148, 0.005653), (-0.61315, -0.789965, -0.001709), (0.005514, -0.002116, -0.999983)22.637, 66.2953, 62.4157
3given(-0.797869, 0.598344, 0.073408), (0.600399, 0.777812, 0.185823), (0.054089, 0.192337, -0.979837)10.9105, -9.471, 54.9261

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 4 / Fragment: UNP P02866 residues 164-281, 30-148 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866

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Sugars , 3 types, 4 molecules

#2: Polysaccharide methyl alpha-D-galactopyranoside-(1-2)-methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 370.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalp[1Me]a1-2DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
[][methyl]{[(1+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide methyl alpha-D-galactopyranoside-(1-2)-methyl alpha-D-galactopyranoside


Type: oligosaccharide / Mass: 370.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalp[1Me]a1-2DGalp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
[][methyl]{[(1+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 81 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growpH: 7 / Details: 13.5% PEG 6K, 1.0M LICL, 0.1M TRIS PH 7.0
Crystal grow
*PLUS
Temperature: 293.5 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.6 mMconA1drop
218 mMoligosaccharide1drop
31 mM1dropMnCl2
41 mM1dropCaCl2
520 mMTris-HCl1drop
650 mM1dropNaCl
710 %PEG60001reservoir
80.1 Mcitric acid1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS / Detector: IMAGE PLATE / Date: Mar 15, 1997 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. obs: 26568 / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.3 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5CNA

5cna


Resolution: 2.75→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: ONLY PARTIAL MODELS FOR THE LIGAND ARE INCLUDED IN SUBUNITS B AND C DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2636 3 %RANDOM
Rwork0.196 ---
obs0.196 26292 99.8 %-
Solvent computationBsol: 39.5 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.3 Å20 Å20 Å2
2---1.97 Å20 Å2
3----0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 82 73 7391
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHBONDS.PROTOPMET.PRO
X-RAY DIFFRACTION2PARMET.PROTOPWATER.PRO
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION4PARWATER.PROTOPSUG.PRO
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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