[English] 日本語
Yorodumi
- PDB-6y0u: Fucosylated Bicyclic peptide bp71 bound to the fucose binding lec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6y0u
TitleFucosylated Bicyclic peptide bp71 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 1.5 Angstrom resolution
Components
  • Fucose-binding lectin
  • bp71
KeywordsANTIBIOTIC / Antimicrobial / Bicyclic / Lectin
Function / homology
Function and homology information


single-species biofilm formation / carbohydrate binding / metal ion binding
Similarity search - Function
Lectin, sugar-binding / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL)
Similarity search - Domain/homology
Chem-ZDC / Fucose-binding lectin / Fucose-binding lectin PA-IIL
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.489 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Citation
Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#1: Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#2: Journal: Rsc Chem Biol / Year: 2021
Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.
Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L.
#3: Journal: Chemrxiv / Year: 2021
Title: Mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography
Authors: Personne, H. / Baeriswyl, S. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.-L.
History
DepositionFeb 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.details / _entity.pdbx_description / _struct.pdbx_descriptor / _struct.title
Revision 1.2Feb 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Feb 1, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conf / struct_conn / struct_ref_seq
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.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _citation.journal_id_ISSN / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_symm_contact.auth_seq_id_1 / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 2.1Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fucose-binding lectin
E: bp71
B: Fucose-binding lectin
F: bp71
C: Fucose-binding lectin
D: Fucose-binding lectin
H: bp71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,43319
Polymers52,2887
Non-polymers1,14512
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-132 kcal/mol
Surface area18370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.821, 56.600, 70.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-501-

HOH

21C-462-

HOH

-
Components

#1: Protein
Fucose-binding lectin / Fucose-binding lectin II (PA-IIL) / Fucose-binding lectin PA-IIL


Mass: 11865.905 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fucose binding Lectin LecB PA-IIL from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Protein/peptide bp71


Mass: 1608.153 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Fucosylated Bicyclic peptide bp71 / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Sugar
ChemComp-ZDC / 3,7-anhydro-2,8-dideoxy-L-glycero-D-gluco-octonic acid


Type: D-saccharide / Mass: 206.193 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H14O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.5 M Ammonium sulfate, 0.1 M Tris pH 8.5, 12% v/v Glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 22, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.489→46.293 Å / Num. obs: 144479 / % possible obs: 92.9 % / Redundancy: 1.74 % / Biso Wilson estimate: 23.591 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.075 / Χ2: 0.93 / Net I/σ(I): 6.16
Reflection shellResolution: 1.489→1.496 Å / Redundancy: 1.59 % / Mean I/σ(I) obs: 1.31 / Num. unique obs: 22185 / CC1/2: 0.578 / Rrim(I) all: 0.844 / Χ2: 0.72 / % possible all: 88.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.84 Å46.29 Å
Translation2.84 Å46.29 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.8.0phasing
PHENIXv1.11.1-2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.489→46.293 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.24 / Phase error: 19.89
RfactorNum. reflection% reflection
Rfree0.1919 7252 5.02 %
Rwork0.1682 --
obs0.1694 144416 92.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.56 Å2 / Biso mean: 23.7915 Å2 / Biso min: 10.68 Å2
Refinement stepCycle: final / Resolution: 1.489→46.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 60 484 4102
Biso mean--18.05 35.49 -
Num. residues----498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063659
X-RAY DIFFRACTIONf_angle_d0.8225000
X-RAY DIFFRACTIONf_chiral_restr0.09634
X-RAY DIFFRACTIONf_plane_restr0.004661
X-RAY DIFFRACTIONf_dihedral_angle_d8.6051192
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.489-1.50570.33232190.3291398381
1.5057-1.52350.34352290.3069422687
1.5235-1.5420.30942320.2877446791
1.542-1.56160.29122340.2693451791
1.5616-1.58210.26792370.2615456693
1.5821-1.60380.27812430.2571459594
1.6038-1.62670.31082390.2531458593
1.6267-1.6510.25732360.2387450092
1.651-1.67680.26032510.2246468096
1.6768-1.70430.24162550.2239480597
1.7043-1.73370.25412440.2164475696
1.7337-1.76520.2642440.2012469096
1.7652-1.79910.19962520.1926470896
1.7991-1.83590.21312540.1765472796
1.8359-1.87580.18772480.1693464495
1.8758-1.91940.18292480.155467695
1.9194-1.96740.18162520.1536467895
1.9674-2.02060.19352530.1531462394
2.0206-2.08010.19122380.1591461994
2.0801-2.14720.17872430.1546449891
2.1472-2.2240.17532370.1438442291
2.224-2.3130.17812240.1491440889
2.313-2.41830.16572460.1483462994
2.4183-2.54570.18322440.1545463795
2.5457-2.70520.16742410.1483469795
2.7052-2.91410.1512490.1446459494
2.9141-3.20730.15122460.1399466095
3.2073-3.67120.15722410.1293456093
3.6712-4.62460.16162290.1442440789
4.6246-46.2930.2162440.1861460793
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9153-0.0235-1.60171.5042-0.33042.4684-0.01950.12850.0858-0.0882-0.0272-0.00130.0024-0.10950.03820.18760.0063-0.00670.16470.00310.1501-28.076420.2242-30.7557
23.5164.2073-1.77198.1552-4.27022.5589-0.0211-0.1113-0.1614-0.1975-0.1776-0.21560.17130.07510.22140.14320.0105-0.00170.1295-0.0210.1199-27.2184.6087-26.5519
3-0.0054-0.0242-0.01519.0376-6.6435.19480.01270.07130.0891-0.4570.08110.21990.2112-0.2295-0.18320.2052-0.0108-0.01610.15470.00310.1435-33.888510.4471-33.3507
41.0401-0.49440.06392.09390.06610.58020.0726-0.01910.036-0.06-0.0446-0.03270.18570.0583-0.08010.1618-0.0146-0.00220.1211-0.00270.1316-30.88311.9717-28.6204
52.4564.7038-3.71199.7028-7.36285.6404-0.06060.09750.0011-0.32740.07280.02240.1996-0.0364-0.03070.2013-0.00070.00980.172-0.01090.1435-24.11275.1679-32.8036
61.19961.8697-2.43794.7481-3.89864.5655-0.04550.12740.1449-0.16650.15070.284-0.005-0.1621-0.10840.1903-0.0214-0.02930.17280.00850.1543-32.457614.5931-32.6193
73.51022.94534.34532.5263.66375.38820.4504-0.1462-1.04310.0655-0.23050.63050.4147-0.3861-0.00190.20410.0017-0.06090.1953-0.02020.3366-42.74535.1542-24.7069
84.90463.3749-0.03553.41610.11130.0119-0.0247-0.0861-0.0454-0.0676-0.0129-0.0395-0.0070.04120.04380.1553-0.0027-0.00630.15170.01190.1137-23.881316.7968-22.6312
90.54380.42550.2741.4740.01160.2840.0063-0.11280.08810.038-0.02340.1030.07330.01830.00530.1599-0.0022-0.00140.1507-0.00420.1341-28.38659.1714-21.5373
100.77690.0741-0.23950.78580.27482.07220.0449-0.0246-0.06230.018-0.011-0.13460.20610.0965-0.01670.1770.0237-0.00730.15780.01090.1867-11.99773.6732-18.0212
116.09412.1514-4.85730.7783-1.73313.8463-0.2149-0.354-0.2216-0.035-0.1104-0.22760.25010.67830.34440.17950.03880.00450.22460.01990.2227-6.17996.7791-15.7396
122.16621.65781.82546.08865.90235.83730.50240.3118-0.0923-0.8838-0.0643-1.2463-0.11780.4495-0.29330.21830.05480.0550.2138-0.03880.34781.78717.9689-23.7663
130.1546-0.27610.06251.37130.53780.62030.02220.01470.0483-0.03850.0018-0.13210.02610.0674-0.03830.12840.0101-0.00340.14140.00660.1399-15.705512.5313-19.4394
141.26150.1470.70040.7943-0.09242.89370.01660.04290.1159-0.0244-0.0339-0.0182-0.18620.09530.03430.1622-0.02070.01320.13230.00140.1685-13.77635.7234-17.2077
155.8334-1.30240.88836.99663.87042.60380.22810.15290.126-0.10340.1524-0.0628-1.2640.0748-0.20470.188-0.0604-0.00790.16140.00010.199-10.764543.2742-15.642
164.71041.88334.97420.7581.80757.37830.6138-0.92610.4030.8268-0.46940.36030.2144-0.4598-0.19970.2396-0.04380.00910.1957-0.02490.1923-14.472936.0251.4198
171.0415-0.46111.07630.98050.28654.25620.00180.12710.204-0.0712-0.0276-0.0849-0.12540.15840.01470.1737-0.0470.01450.12690.02410.1814-14.706538.642-18.6653
188.36464.4559-3.06093.618-3.95246.00260.1511-0.4225-0.0650.3735-0.02930.0255-0.26890.2532-0.05530.1671-0.01980.0070.1682-0.00970.1786-0.601835.0199-7.9183
190.06360.17220.02140.40630.230.4627-0.00370.0065-0.0065-0.0378-0.0046-0.0473-0.05040.02260.02060.1344-0.01480.00450.13810.00440.1332-17.110628.5068-13.9126
206.08730.43844.73151.85090.96964.7693-0.009-0.1211-0.19980.0442-0.00350.05380.0899-0.19470.00030.1679-0.01350.04370.14220.00590.135-28.835419.2109-3.3705
211.5328-2.4711.33667.1931-5.29114.98270.03850.0409-0.0110.14350.0550.2721-0.0748-0.1037-0.08450.17260.00780.01080.09-0.04420.0988-32.419832.0317-4.9698
222.4691-1.97812.4028.231-3.59332.90950.0901-0.0450.15630.6460.15780.48-0.4186-0.244-0.14570.20150.00960.02180.1512-0.00180.1646-35.187932.80240.5316
238.6-2.7273-1.69484.40471.45342.9714-0.00670.21250.3168-0.0231-0.0065-0.0237-0.31490.0034-0.01030.25180.0112-0.00760.15720.00330.1775-31.400942.6612-14.6814
245.4728-5.58825.86975.7001-5.98886.1993-0.1048-0.06930.01470.5990.08070.1461-0.5479-0.04490.12290.23660.0110.01260.1383-0.02490.1444-26.706734.0433-0.4051
258.5297-6.34968.74045.0007-7.01179.8290.0072-0.2383-0.08430.20080.1940.2812-0.0979-0.3443-0.39430.16950.00820.03230.15670.00360.1725-33.295823.1868-1.0684
263.4196-3.5339-3.85873.69924.08424.6327-0.03880.42550.40580.3968-0.14291.6334-0.3791-0.92270.25170.23420.0590.04850.2129-0.0170.4027-44.696232.8307-10.6102
274.6282-2.38040.59442.8789-0.20890.14820.01510.0881-0.02330.0098-0.04480.04-0.0070.00290.02890.1375-0.00740.01230.14650.00360.1182-24.615123.0703-11.2572
281.6447-0.86670.40331.2677-0.25051.08410.02640.0564-0.1883-0.08190.02470.1679-0.0895-0.0418-0.10540.1538-0.00190.00120.1437-0.00380.1706-30.099830.1841-12.7503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )A1 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 25 )A13 - 25
3X-RAY DIFFRACTION3chain 'A' and (resid 26 through 34 )A26 - 34
4X-RAY DIFFRACTION4chain 'A' and (resid 35 through 47 )A35 - 47
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 56 )A48 - 56
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 69 )A57 - 69
7X-RAY DIFFRACTION7chain 'A' and (resid 70 through 74 )A70 - 74
8X-RAY DIFFRACTION8chain 'A' and (resid 75 through 95 )A75 - 95
9X-RAY DIFFRACTION9chain 'A' and (resid 96 through 114 )A96 - 114
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 61 )B1 - 61
11X-RAY DIFFRACTION11chain 'B' and (resid 62 through 69 )B62 - 69
12X-RAY DIFFRACTION12chain 'B' and (resid 70 through 74 )B70 - 74
13X-RAY DIFFRACTION13chain 'B' and (resid 75 through 114 )B75 - 114
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 34 )C1 - 34
15X-RAY DIFFRACTION15chain 'C' and (resid 35 through 42 )C35 - 42
16X-RAY DIFFRACTION16chain 'C' and (resid 43 through 47 )C43 - 47
17X-RAY DIFFRACTION17chain 'C' and (resid 48 through 68 )C48 - 68
18X-RAY DIFFRACTION18chain 'C' and (resid 69 through 74 )C69 - 74
19X-RAY DIFFRACTION19chain 'C' and (resid 75 through 114 )C75 - 114
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 12 )D1 - 12
21X-RAY DIFFRACTION21chain 'D' and (resid 13 through 34 )D13 - 34
22X-RAY DIFFRACTION22chain 'D' and (resid 35 through 42 )D35 - 42
23X-RAY DIFFRACTION23chain 'D' and (resid 43 through 48 )D43 - 48
24X-RAY DIFFRACTION24chain 'D' and (resid 49 through 56 )D49 - 56
25X-RAY DIFFRACTION25chain 'D' and (resid 57 through 68 )D57 - 68
26X-RAY DIFFRACTION26chain 'D' and (resid 69 through 74 )D69 - 74
27X-RAY DIFFRACTION27chain 'D' and (resid 75 through 95 )D75 - 95
28X-RAY DIFFRACTION28chain 'D' and (resid 96 through 114 )D96 - 114

+
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://pdbjlvh1.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