[English] 日本語
Yorodumi
- PDB-5i8x: Bicyclic antimibrocial peptides -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i8x
TitleBicyclic antimibrocial peptides
Components
  • DLS-LYS-CYS-LYS-LEU-CYS-LYS-LYS-NH2
  • Fucose-binding lectin
KeywordsSUGAR BINDING PROTEIN / Bicycle / Antimicrobial peptide / pseudomonas aeruginosa / biofilm
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 / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / Jelly Rolls / Sandwich / Mainly Beta
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 / Resolution: 1.89 Å
AuthorsDi Bonaventura, I. / Jin, X. / Visini, R. / Michaud, G. / Robadey, M. / Koehler, T. / van Delden, C. / Stocker, A. / Darbre, T. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Chem Sci / Year: 2017
Title: Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms.
Authors: Di Bonaventura, I. / Jin, X. / Visini, R. / Probst, D. / Javor, S. / Gan, B.H. / Michaud, G. / Natalello, A. / Doglia, S.M. / Kohler, T. / van Delden, C. / Stocker, A. / Darbre, T. / Reymond, J.L.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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.type_symbol / _pdbx_audit_support.funding_organization / _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_auth_seq_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_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _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.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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.type / _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_seq_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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fucose-binding lectin
B: Fucose-binding lectin
C: Fucose-binding lectin
D: Fucose-binding lectin
E: DLS-LYS-CYS-LYS-LEU-CYS-LYS-LYS-NH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,13317
Polymers47,9875
Non-polymers1,14512
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-111 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.424, 79.202, 52.627
Angle α, β, γ (deg.)90.00, 94.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AN451_21855, AN453_22575, AN455_18155, AN456_19070, AN457_11175, AN458_15745, AN460_27980, AN462_17515, AOD73_08535, AOX61_ ...Gene: lecB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AN451_21855, AN453_22575, AN455_18155, AN456_19070, AN457_11175, AN458_15745, AN460_27980, AN462_17515, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, APG04_23970, APG05_03535, APG06_28020, APG07_27985, ATC05_02360, ERS445055_01627, PA8380_17510, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713, PAO1OR1608
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Protein/peptide DLS-LYS-CYS-LYS-LEU-CYS-LYS-LYS-NH2


Mass: 1048.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: 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: obtained synthetically / Formula: C8H14O6
#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 / Water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M Ammonium Acetate 0.1 M Sodium Acetate 30 w/v PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.89→48.273 Å / Num. obs: 31514 / % possible obs: 98.9 % / Redundancy: 3.33 % / CC1/2: 0.983 / Rmerge(I) obs: 0.184 / Net I/σ(I): 6.13
Reflection shellResolution: 1.89→2 Å / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4900 / CC1/2: 0.727 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CE8

4ce8


Resolution: 1.89→48.273 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.91 / Phase error: 22.33
RfactorNum. reflection% reflection
Rfree0.2228 2947 4.98 %
Rwork0.1828 --
obs0.1848 31491 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.89→48.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 60 328 3736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063466
X-RAY DIFFRACTIONf_angle_d0.8844755
X-RAY DIFFRACTIONf_dihedral_angle_d9.9291987
X-RAY DIFFRACTIONf_chiral_restr0.064607
X-RAY DIFFRACTIONf_plane_restr0.004632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.889-1.91990.32071100.2822123X-RAY DIFFRACTION75
1.9199-1.9530.30721300.25662659X-RAY DIFFRACTION93
1.953-1.98850.25841370.23792639X-RAY DIFFRACTION93
1.9885-2.02680.2781410.23672689X-RAY DIFFRACTION94
2.0268-2.06820.30181400.22922635X-RAY DIFFRACTION94
2.0682-2.11310.26871430.22492703X-RAY DIFFRACTION94
2.1131-2.16230.22921410.21522660X-RAY DIFFRACTION95
2.1623-2.21640.25091420.21512712X-RAY DIFFRACTION95
2.2164-2.27630.26551420.20532700X-RAY DIFFRACTION95
2.2763-2.34330.27581360.20392618X-RAY DIFFRACTION95
2.3433-2.41890.22761400.19882700X-RAY DIFFRACTION94
2.4189-2.50530.23161410.19682665X-RAY DIFFRACTION94
2.5053-2.60570.2151380.19952621X-RAY DIFFRACTION94
2.6057-2.72420.25581450.18452771X-RAY DIFFRACTION97
2.7242-2.86780.2221500.17512800X-RAY DIFFRACTION99
2.8678-3.04750.20951490.16152797X-RAY DIFFRACTION99
3.0475-3.28270.17511500.15692789X-RAY DIFFRACTION99
3.2827-3.6130.20531440.14362742X-RAY DIFFRACTION97
3.613-4.13560.20681390.14082751X-RAY DIFFRACTION97
4.1356-5.20940.1491380.14082677X-RAY DIFFRACTION95
5.2094-48.28920.18861510.16042807X-RAY DIFFRACTION99
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)
11.9596-0.7016-0.25361.9380.77642.62040.050.0364-0.05820.0776-0.0240.14150.3106-0.2349-0.03040.0992-0.0264-0.00450.1172-0.00660.0981-2.59483.4831-6.9005
27.35970.2654-0.20932.0137.23394.70540.17690.12050.1799-0.2747-0.52840.58250.1271-0.69760.39760.2442-0.0013-0.00180.1682-0.00070.1134-8.99031.9181-1.6507
30.7957-1.07830.11023.89340.92423.20060.0322-0.0538-0.1144-0.07990.04460.12910.2103-0.0881-0.03430.0681-0.03610.01430.13180.00550.1373-3.46475.1473-3.4143
46.63843.945-4.62517.1237-3.50059.9312-0.0564-0.0780.59260.1105-0.02190.9731-0.4045-0.47270.08220.1509-0.0189-0.01860.207-0.00170.2345-15.204313.8814-8.622
50.959-0.0491-0.45960.11490.46631.2005-0.04230.11330.0384-0.0470.0227-0.01030.06-0.08230.01140.0903-0.0159-0.00730.09760.00320.11643.28579.2132-9.5697
67.83913.62531.64812.59491.07552.11310.0909-0.2528-0.0018-0.0683-0.09-0.2381-0.0827-0.056-0.02140.13360.0243-0.01670.0706-0.00460.14278.566423.2445-22.3824
71.7470.47242.12753.12082.40354.60440.04250.1251-0.15-0.21250.1865-0.4098-0.0468-0.0445-0.18940.0679-0.00780.02340.10250.01680.096711.684212.4223-34.1647
82.93811.87491.02048.94172.91151.9332-0.20780.33240.3155-0.3480.35310.2917-0.4859-0.111-0.13150.20970.010.02960.16380.04120.12715.828921.769-33.9079
93.8364-0.8549-1.83124.01353.60756.26670.21250.17750.4183-0.8776-0.40360.0493-0.7017-0.43010.1760.19890.0413-0.04390.12970.03580.14268.573721.2381-37.9714
102.64352.43191.39353.53663.16833.0617-0.06320.0340.1761-0.5112-0.01070.0711-0.21140.2031-0.00320.1006-0.0103-0.00930.10910.01190.094313.897212.0075-36.6545
111.00440.4141-0.25544.45191.53813.3149-0.34290.11810.53770.07740.03320.6757-0.4711-0.43110.36150.12970.0358-0.02890.13570.00240.18876.07322.9741-29.3904
123.89130.9982.05021.62671.31074.1511-0.10580.0214-0.0811-0.0570.109-0.0104-0.1508-0.1712-00.08730.00110.01740.0840.01360.1048.871213.7666-23.7671
131.5405-2.21982.95565.9826-1.61168.1625-0.1785-0.2591-0.0619-0.01620.25540.26430.1497-0.6055-0.0460.11150.00040.01770.14520.00720.0986-0.11233.3227-31.0824
141.4740.6217-0.14781.28680.15560.05950.02780.11990.0578-0.1642-0.0709-0.10590.02280.10540.0580.14480.0049-0.020.09460.02740.08316.45816.8888-26.2566
152.45911.73550.8532.63192.97474.36620.0165-0.0015-0.15290.08410.0903-0.11020.31430.1295-0.07690.12730.01640.00290.10880.04210.117118.5313-3.2641-19.2386
163.6232.584-0.44795.6984-0.25590.8128-0.08510.0477-0.0911-0.09330.0202-0.10510.12570.16130.07010.10930.01360.02010.10820.00890.050126.09734.3645-27.886
176.81844.342-1.08676.3809-3.45533.2779-0.09080.0787-0.21750.07470.16340.06240.515-0.0397-0.11870.2187-0.00730.02050.0782-0.00560.104229.2366-0.6999-30.454
184.1611-2.0462-2.39457.2722.81583.85630.4449-0.06540.9625-0.44240.2226-0.4712-0.45790.076-0.55120.1299-0.01330.05670.19410.03770.187228.559218.2461-31.5783
192.41212.586-0.00817.1119-0.06672.64180.00640.0348-0.0904-0.07190.0337-0.38280.09850.239-0.04690.08280.00090.01010.13150.00640.088521.90532.853-33.3539
201.83330.9261-0.45824.2887-0.34212.19980.081-0.2479-0.28580.1-0.08-0.52480.25090.1408-0.04150.15140.0291-0.00540.118-0.04870.169624.1382-3.8089-22.3352
216.19791.4706-0.60220.4241-0.18620.7738-0.0003-0.24930.0474-0.0428-0.0301-0.00960.00730.03080.05790.12640.0155-0.00820.08970.01050.111419.84216.493-20.0085
224.02781.0966-0.88334.7962-2.47961.3203-0.1636-0.1139-0.04690.55530.0163-0.3032-0.05470.01520.14690.16630.0161-0.01090.1109-0.02450.161430.426616.7729-18.5461
236.20994.18271.37983.63310.35530.69850.0466-0.01940.04570.02240.03290.0292-0.0735-0.0222-0.08620.10630.00280.01670.0611-0.01420.104115.41513.4784-27.2102
240.44130.3425-0.84513.5833-0.6941.60310.0547-0.01710.05380.0862-0.01310.1455-0.07470.0354-0.04090.0671-0.0134-0.04510.1354-0.02870.108214.279214.7354-0.8883
251.3897-1.2209-0.07452.3548-2.37314.6090.1837-0.33590.30780.2686-0.4113-0.2811-0.26980.27740.28010.1137-0.0119-0.00280.2226-0.03010.181518.068216.46526.9358
262.11371.2487-0.64664.9188-1.73431.5339-0.0083-0.12370.03030.1597-0.0253-0.1199-0.10650.12070.05570.1010.0095-0.01090.1225-0.02710.076313.925213.44443.8208
270.37530.152-0.62641.6362-0.55091.59820.002-0.20980.16030.00010.057-0.1562-0.00730.0963-0.03180.0849-0.0175-0.01080.1047-0.02550.076414.648911.528-6.5543
280.46340.362-0.5060.3262-0.20491.0345-0.02190.0553-0.1406-0.0848-0.01550.01260.01820.12820.06880.11380.003-0.02230.1551-0.02750.124114.16227.1535-2.0221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 114 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 12 )
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 25 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 34 )
9X-RAY DIFFRACTION9chain 'B' and (resid 35 through 42 )
10X-RAY DIFFRACTION10chain 'B' and (resid 43 through 56 )
11X-RAY DIFFRACTION11chain 'B' and (resid 57 through 69 )
12X-RAY DIFFRACTION12chain 'B' and (resid 70 through 95 )
13X-RAY DIFFRACTION13chain 'B' and (resid 96 through 104 )
14X-RAY DIFFRACTION14chain 'B' and (resid 105 through 114 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 12 )
16X-RAY DIFFRACTION16chain 'C' and (resid 13 through 34 )
17X-RAY DIFFRACTION17chain 'C' and (resid 35 through 42 )
18X-RAY DIFFRACTION18chain 'C' and (resid 43 through 47 )
19X-RAY DIFFRACTION19chain 'C' and (resid 48 through 56 )
20X-RAY DIFFRACTION20chain 'C' and (resid 57 through 68 )
21X-RAY DIFFRACTION21chain 'C' and (resid 69 through 95 )
22X-RAY DIFFRACTION22chain 'C' and (resid 96 through 104 )
23X-RAY DIFFRACTION23chain 'C' and (resid 105 through 114 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 25 )
25X-RAY DIFFRACTION25chain 'D' and (resid 26 through 42 )
26X-RAY DIFFRACTION26chain 'D' and (resid 43 through 69 )
27X-RAY DIFFRACTION27chain 'D' and (resid 70 through 95 )
28X-RAY DIFFRACTION28chain 'D' and (resid 96 through 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://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