[English] 日本語
Yorodumi
- PDB-2vmd: Structure of the complex of discoidin II from Dictyostelium disco... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vmd
TitleStructure of the complex of discoidin II from Dictyostelium discoideum with beta-methyl-galactose
ComponentsDISCOIDIN-2Discoidin domain
KeywordsCELL ADHESION / DDR / LECTIN / AGGREGATION
Function / homology
Function and homology information


spore wall / N-acetylgalactosamine binding / protein complex involved in cell adhesion / galactoside binding / oligosaccharide binding / polysaccharide binding / phagocytic vesicle / cytoskeleton organization / extracellular matrix / response to bacterium ...spore wall / N-acetylgalactosamine binding / protein complex involved in cell adhesion / galactoside binding / oligosaccharide binding / polysaccharide binding / phagocytic vesicle / cytoskeleton organization / extracellular matrix / response to bacterium / cell-cell adhesion / carbohydrate binding / vesicle / cell adhesion / metal ion binding / 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 factor 5/8 C-terminal domain, discoidin domain / 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 factor 5/8 C-terminal domain, discoidin domain / 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 / methyl beta-D-galactopyranoside / Discoidin-2
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAragao, K.S. / Satre, M. / Imberty, A. / Varrot, A.
CitationJournal: Proteins / Year: 2008
Title: Structure Determination of Discoidin II from Dictyostelium Discoideum and Carbohydrate Binding Properties of the Lectin Domain.
Authors: Aragao, K.S. / Satre, M. / Imberty, A. / Varrot, A.
History
DepositionJan 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DISCOIDIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4427
Polymers28,6061
Non-polymers8366
Water4,107228
1
A: DISCOIDIN-2
hetero molecules

A: DISCOIDIN-2
hetero molecules

A: DISCOIDIN-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,32621
Polymers85,8173
Non-polymers2,50918
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area16140 Å2
ΔGint-29.7 kcal/mol
Surface area27420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.140, 81.140, 259.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-499-

CL

21A-2006-

HOH

31A-2013-

HOH

41A-2014-

HOH

51A-2015-

HOH

61A-2080-

HOH

71A-2200-

HOH

81A-2216-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein DISCOIDIN-2 / Discoidin domain / DISCOIDIN II


Mass: 28605.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX2 / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: P42530
#4: Sugar ChemComp-MBG / methyl beta-D-galactopyranoside / METHYL-BETA-GALACTOSE / methyl beta-D-galactoside / methyl D-galactoside / methyl galactoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DGalp[1Me]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-methyl-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 5 types, 233 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / Polyethylene glycol


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer details2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY) -ETHANOL (1PG):

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.7 % / Description: NONE
Crystal growpH: 7.5 / Details: 25 % PEG550 MME, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.9→36.7 Å / Num. obs: 26194 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.7
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 4.06 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.35 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VM9

2vm9


Resolution: 1.9→36.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.276 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5 ARE DISORDERED.DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1326 5.1 %RANDOM
Rwork0.178 ---
obs0.181 24868 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20.79 Å20 Å2
2--1.58 Å20 Å2
3----2.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 37 228 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212075
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4941.9252814
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4265253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85624.51102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82715327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3191511
X-RAY DIFFRACTIONr_chiral_restr0.1080.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2841
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21423
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.2100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8781.51274
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46522040
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3613895
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4834.5774
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.327 94
Rwork0.257 1745

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more