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- PDB-1tei: STRUCTURE OF CONCANAVALIN A COMPLEXED TO BETA-D-GLCNAC (1,2)ALPHA... -

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Entry
Database: PDB / ID: 1tei
TitleSTRUCTURE OF CONCANAVALIN A COMPLEXED TO BETA-D-GLCNAC (1,2)ALPHA-D-MAN-(1,6)[BETA-D-GLCNAC(1,2)ALPHA-D-MAN (1,6)]ALPHA-D-MAN
ComponentsCONCANAVALIN A
KeywordsLECTIN / CONCANAVALIN A / PENTASACCHARIDE 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, beta chain, Mn/Ca-binding site / Legume lectin domain / 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, 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
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNaismith, J.H. / Moothoo, D.N.
Citation
Journal: Glycobiology / Year: 1998
Title: Concanavalin A distorts the beta-GlcNAc-(1-->2)-Man linkage of beta-GlcNAc-(1-->2)-alpha-Man-(1-->3)-[beta-GlcNAc-(1-->2)-alpha-Man- (1-->6)]-Man upon binding.
Authors: Moothoo, D.N. / Naismith, J.H.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Structural Basis of Trimannoside Recognition by Concanavalin A
Authors: Naismith, J.H. / Field, R.A.
History
DepositionMay 28, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _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 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.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 / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / 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
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
E: CONCANAVALIN A
F: CONCANAVALIN A
G: CONCANAVALIN A
H: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,02632
Polymers204,9798
Non-polymers8,04724
Water1,36976
1
A: CONCANAVALIN A
B: CONCANAVALIN A
C: CONCANAVALIN A
D: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,51316
Polymers102,4904
Non-polymers4,02312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16540 Å2
ΔGint-31 kcal/mol
Surface area33160 Å2
MethodPISA
2
E: CONCANAVALIN A
F: CONCANAVALIN A
G: CONCANAVALIN A
H: CONCANAVALIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,51316
Polymers102,4904
Non-polymers4,02312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16360 Å2
ΔGint-32 kcal/mol
Surface area33310 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33540 Å2
ΔGint-64 kcal/mol
Surface area65830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.500, 122.800, 124.600
Angle α, β, γ (deg.)90.00, 134.20, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2651, -0.0972, -0.9593), (-0.0937, -0.9928, 0.0747), (-0.9597, 0.07, -0.2723)30.3718, 3.9135, 40.0021
2given(-0.4528, 0.5989, 0.6605), (0.5779, -0.367, 0.7289), (0.679, 0.7118, -0.18)57.4044, -23.7627, -26.0853
3given(-0.8119, -0.5064, 0.2905), (-0.5097, 0.3723, -0.7756), (0.2847, -0.7778, 0.5604)72.3088, 21.4369, -9.6917
4given(0.9153, -0.3777, -0.1399), (0.3836, 0.7117, 0.5885), (-0.1227, -0.5923, 0.7963)48.3804, 3.2804, -41.798
5given(0.4206, 0.294, -0.8583), (-0.5033, -0.7115, -0.4904), (-0.7549, 0.6382, -0.1512)68.9231, 39.6984, -15.4542
6given(-0.726, 0.5761, 0.3755), (0.6346, 0.3509, 0.6887), (0.265, 0.7383, -0.6203)113.2065, -7.3115, -55.9725
7given(-0.607, -0.4771, 0.6356), (-0.5279, -0.3558, -0.7712), (0.594, -0.8036, -0.0359)108.3815, 40.9961, -69.7647

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Components

#1: Protein
CONCANAVALIN A / CON A


Mass: 25622.385 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-1-2-1-2/a3-b1_a6-d1_b2-c1_d2-e1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.36 Å3/Da / Density % sol: 46 %
Crystal growpH: 5.5 / Details: POLYETHYLENE GLYCOL 15%, pH 5.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
26 mg/mlprotein1drop
31 mM1dropMnCl2
41 mM1dropCaCl2
515 %PEG60001reservoir
1sugar1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MAC Science DIP-2000 / Detector: IMAGE PLATE / Date: Oct 29, 1996 / Details: MIRRORS, MACSCIENCE
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. obs: 53516 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.094
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 95.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.337

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5CNA

5cna


Resolution: 2.7→25 Å / Isotropic thermal model: RESTRAINED / Cross valid method: X-PLOR / σ(F): 0
Details: ATOMS WITH ZERO OCCUPANCY (443 OUT OF 14472 PROTEIN ATOMS, 25 OUT OF 496 SUGAR ATOMS) ARE STEREOCHEMICALLY MODELED. THE LOOP AT RESIDUE 120 IS KNOWN TO BE PARTIALLY CLEAVED IN THE PROTEIN ...Details: ATOMS WITH ZERO OCCUPANCY (443 OUT OF 14472 PROTEIN ATOMS, 25 OUT OF 496 SUGAR ATOMS) ARE STEREOCHEMICALLY MODELED. THE LOOP AT RESIDUE 120 IS KNOWN TO BE PARTIALLY CLEAVED IN THE PROTEIN AND WAS NOT LOCATED IN INTERPRETABLE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 4470 10 %RANDOM
Rwork0.179 ---
obs0.179 50737 97.1 %-
Displacement parametersBiso mean: 23.3 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14472 0 512 76 15060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.746
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.439
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it28.6
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it29.6
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSWeight Biso : 3 / Weight position: 60
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 8
Rfactor% reflection
Rfree0.3141 10 %
Rwork0.2498 -
obs-95.4 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.439
LS refinement shell
*PLUS
Rfactor obs: 0.2498

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