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- PDB-2wn3: Crystal structure of Discoidin I from Dictyostelium discoideum in... -

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Basic information

Entry
Database: PDB / ID: 2wn3
TitleCrystal structure of Discoidin I from Dictyostelium discoideum in complex with the disaccharide GalNAc beta 1-3 galactose, at 1.6 A resolution.
ComponentsDISCOIDIN-1 SUBUNIT A
KeywordsCELL ADHESION / TYPE-H LECTIN / DISCOIDIN DOMAIN / LECTIN
Function / homology
Function and homology information


lectin-induced modified bacterial internalization / lipooligosaccharide binding / response to catechin / protein localization to cell cortex / asexual reproduction / N-acetylgalactosamine binding / response to curcumin / protein complex involved in cell adhesion / symbiont cell surface / oligosaccharide binding ...lectin-induced modified bacterial internalization / lipooligosaccharide binding / response to catechin / protein localization to cell cortex / asexual reproduction / N-acetylgalactosamine binding / response to curcumin / protein complex involved in cell adhesion / symbiont cell surface / oligosaccharide binding / regulation of protein complex stability / cortical cytoskeleton organization / polysaccharide binding / intracellular vesicle / cell-substrate adhesion / mitotic cytokinesis / phagocytic vesicle / cytoskeleton organization / extracellular matrix / response to bacterium / cell-cell adhesion / cell cortex / regulation of gene expression / carbohydrate binding / cell adhesion / cell surface / cytosol / cytoplasm
Similarity search - Function
: / Immunoglobulin-like - #2080 / H-type lectin domain / H-type lectin domain superfamily / H-type lectin domain / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like ...: / Immunoglobulin-like - #2080 / H-type lectin domain / H-type lectin domain superfamily / H-type lectin domain / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-1PG / Discoidin-1 subunit A
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsMathieu, S. / Imberty, A. / Varrot, A.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Discoidin I from Dictyostelium Discoideum and Interactions with Oligosaccharides: Specificity, Affinity, Crystal Structures and Comparison with Discoidin II.
Authors: Mathieu, S. / Saboia Aragao, K. / Imberty, A. / Varrot, A.
History
DepositionJul 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_struct_special_symmetry / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _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_label_asym_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_struct_special_symmetry.label_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DISCOIDIN-1 SUBUNIT A
B: DISCOIDIN-1 SUBUNIT A
C: DISCOIDIN-1 SUBUNIT A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,15116
Polymers85,0643
Non-polymers2,08713
Water20,1951121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-85.2 kcal/mol
Surface area26840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.580, 274.000, 85.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2218-

HOH

21B-2037-

HOH

31B-2039-

HOH

41B-2351-

HOH

51C-2077-

HOH

61C-2241-

HOH

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein DISCOIDIN-1 SUBUNIT A / DISCOIDIN-1 SUBUNIT ALPHA / DISCOIDIN I CHAIN A


Mass: 28354.576 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX2 / Plasmid: PPROEX-HTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA 2 (DE3) PLYSS / References: UniProt: P02886
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+1)][b-D-GalpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 1131 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1121 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFIRST RESIDUE IS ADDED FOLLOWING THE CLEAVAGE OF THE N TERMINAL HIS TAG

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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: 2.5 Å3/Da / Density % sol: 50.77 % / Description: NONE
Crystal growpH: 7.5
Details: 100MM HEPES PH7.5, LI2SO4 1.2M, 20% GLYCEROL AS CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.95375
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95375 Å / Relative weight: 1
ReflectionResolution: 1.59→43.73 Å / Num. obs: 114648 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.8
Reflection shellResolution: 1.59→1.67 Å / Redundancy: 3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W94

2w94


Resolution: 1.59→137 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.325 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18023 5754 5 %RANDOM
Rwork0.15159 ---
obs0.15301 108859 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.576 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0.98 Å20 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.59→137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5967 0 131 1121 7219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226295
X-RAY DIFFRACTIONr_bond_other_d0.0010.024050
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9318603
X-RAY DIFFRACTIONr_angle_other_deg0.89739847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0955782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23424.331314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.13615947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2311539
X-RAY DIFFRACTIONr_chiral_restr0.1020.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021326
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8721.53813
X-RAY DIFFRACTIONr_mcbond_other0.2771.51555
X-RAY DIFFRACTIONr_mcangle_it1.47526204
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.27532482
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4514.52386
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: 1.59→1.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 437 -
Rwork0.295 7888 -
obs--98.08 %

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