[English] 日本語
Yorodumi
- PDB-2vxj: CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL13BGAL14GLC ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vxj
TitleCRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH AGAL13BGAL14GLC AT 1.9 A RESOLUTION
ComponentsPA-I GALACTOPHILIC LECTIN
KeywordsSUGAR BINDING PROTEIN / LECTIN / GLOBOSIDE
Function / homology
Function and homology information


heterophilic cell-cell adhesion / carbohydrate binding / periplasmic space / cell surface / cytoplasm
Similarity search - Function
PA-IL-like / PA-IL-like protein / Galactose-binding lectin / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / PA-I galactophilic lectin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBlanchard, B. / Nurisso, A. / Hollville, E. / Tetaud, C. / Wiels, J. / Pokorna, M. / Wimmerova, M. / Varrot, A. / Imberty, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Basis of the Preferential Binding for Globo-Series Glycosphingolipids Displayed by Pseudomonas Aeruginosa Lectin I.
Authors: Blanchard, B. / Nurisso, A. / Hollville, E. / Tetaud, C. / Wiels, J. / Pokorna, M. / Wimmerova, M. / Varrot, A. / Imberty, A.
History
DepositionJul 4, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PA-I GALACTOPHILIC LECTIN
B: PA-I GALACTOPHILIC LECTIN
C: PA-I GALACTOPHILIC LECTIN
D: PA-I GALACTOPHILIC LECTIN
E: PA-I GALACTOPHILIC LECTIN
F: PA-I GALACTOPHILIC LECTIN
G: PA-I GALACTOPHILIC LECTIN
H: PA-I GALACTOPHILIC LECTIN
I: PA-I GALACTOPHILIC LECTIN
J: PA-I GALACTOPHILIC LECTIN
K: PA-I GALACTOPHILIC LECTIN
L: PA-I GALACTOPHILIC LECTIN
M: PA-I GALACTOPHILIC LECTIN
N: PA-I GALACTOPHILIC LECTIN
O: PA-I GALACTOPHILIC LECTIN
P: PA-I GALACTOPHILIC LECTIN
Q: PA-I GALACTOPHILIC LECTIN
R: PA-I GALACTOPHILIC LECTIN
S: PA-I GALACTOPHILIC LECTIN
T: PA-I GALACTOPHILIC LECTIN
U: PA-I GALACTOPHILIC LECTIN
V: PA-I GALACTOPHILIC LECTIN
W: PA-I GALACTOPHILIC LECTIN
X: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)320,81193
Polymers306,48324
Non-polymers14,32869
Water54,8743046
1
A: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3153
Polymers12,7701
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3153
Polymers12,7701
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3153
Polymers12,7701
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4395
Polymers12,7701
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3153
Polymers12,7701
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3153
Polymers12,7701
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4395
Polymers12,7701
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3955
Polymers12,7701
Non-polymers6254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3153
Polymers12,7701
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
17
Q: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4395
Polymers12,7701
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
18
R: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3153
Polymers12,7701
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
19
S: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
20
T: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3153
Polymers12,7701
Non-polymers5452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
21
U: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
22
V: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
23
W: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4395
Polymers12,7701
Non-polymers6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
24
X: PA-I GALACTOPHILIC LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3774
Polymers12,7701
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.184, 86.521, 119.078
Angle α, β, γ (deg.)93.93, 98.16, 90.08
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX

#1: Protein ...
PA-I GALACTOPHILIC LECTIN / PA-IL / GALACTOSE-BINDING LECTIN


Mass: 12770.137 Da / Num. of mol.: 24 / Fragment: RESIDUES 2-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET25B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05097

-
Sugars , 4 types, 25 molecules

#2: Polysaccharide...
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 21
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][a2112h-1a_1-5]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][a-D-Galp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 3090 molecules

#5: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3046 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsN-TERMINAL METHIONINE CLEAVED

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.3 % / Description: NONE
Crystal growpH: 4.6 / Details: 10% PEG 5000 MME, 0.025M KSCN, 0.1M NAAC PH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 30, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→55.22 Å / Num. obs: 230909 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 2.26 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.45
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.08 / % possible all: 89.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1L7L

1l7l


Resolution: 1.9→55 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.886 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 11594 5 %RANDOM
Rwork0.185 ---
obs0.188 219312 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.12 Å20.01 Å2
2--1.33 Å20.23 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.9→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21559 0 920 3046 25525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02223113
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214692
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.96531670
X-RAY DIFFRACTIONr_angle_other_deg0.914335874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47152891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83225.834989
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.807153112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.4081550
X-RAY DIFFRACTIONr_chiral_restr0.0920.23628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0225699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024235
X-RAY DIFFRACTIONr_nbd_refined0.1930.24059
X-RAY DIFFRACTIONr_nbd_other0.1950.215335
X-RAY DIFFRACTIONr_nbtor_refined0.1710.211274
X-RAY DIFFRACTIONr_nbtor_other0.0850.211368
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.22377
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1150.282
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.263
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8371.514839
X-RAY DIFFRACTIONr_mcbond_other0.2151.56024
X-RAY DIFFRACTIONr_mcangle_it1.256222887
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.92939961
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8114.58772
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% reflection
Rfree0.295 825 -
Rwork0.229 15321 -
obs--88.83 %

+
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