[English] 日本語
Yorodumi
- PDB-6q8g: Structure of Fucosylated D-antimicrobial peptide SB8 in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q8g
TitleStructure of Fucosylated D-antimicrobial peptide SB8 in complex with the Fucose-binding lectin PA-IIL at 1.190 Angstrom resolution
Components
  • Fucose-binding lectin
  • SB8
KeywordsANTIBIOTIC / Antimicrobial / Lectin / Complex
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
AMINO GROUP / Chem-ZDC / polypeptide(D) / polypeptide(D) (> 10) / 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: 1.19 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes.
Authors: Baeriswyl, S. / Gan, B.H. / Siriwardena, T.N. / Visini, R. / Robadey, M. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.L.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 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.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 1.3Jan 24, 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
E: SB8
B: Fucose-binding lectin
F: SB8
C: Fucose-binding lectin
G: SB8
D: Fucose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,87721
Polymers50,7007
Non-polymers1,17714
Water10,611589
1
A: Fucose-binding lectin
E: SB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3317
Polymers12,9882
Non-polymers3425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fucose-binding lectin
F: SB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2515
Polymers12,9882
Non-polymers2623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fucose-binding lectin
G: SB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5217
Polymers12,9882
Non-polymers5335
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Fucose-binding lectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7752
Polymers11,7351
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.445, 72.085, 123.593
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Polypeptide(D) / Sugars , 3 types, 11 molecules ABCDEFG

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


Mass: 11734.707 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Fucose-binding lectin PA-IIL Lectin B from Pseudomonas aeruginosa
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: lecB, C0043_24310, C0044_25260, C0046_23510, CAZ10_21840, CW299_25270, DI492_13230, DT376_00595, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS
#2: Polypeptide(D) SB8


Mass: 1253.666 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Fucosylated D-antimicrobial peptide SB8 / Source: (synth.) synthetic construct (others)
#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

-
Non-polymers , 3 types, 599 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris pH 8.5, 0.5% w/v Polyethylene glycol monomethyl ether 5,000

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2017
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.19→46.916 Å / Num. obs: 276822 / % possible obs: 88.6 % / Redundancy: 3.01 % / Rrim(I) all: 0.062 / Net I/σ(I): 11.74
Reflection shellResolution: 1.19→1.196 Å / Mean I/σ(I) obs: 0.82 / Num. unique obs: 189

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.89 Å46.92 Å
Translation2.89 Å46.92 Å

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC

1oxc


Resolution: 1.19→46.916 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0.96 / Phase error: 16.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1605 13820 4.99 %
Rwork0.1447 262883 -
obs0.1455 276703 88.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.09 Å2 / Biso mean: 19.3658 Å2 / Biso min: 8.52 Å2
Refinement stepCycle: final / Resolution: 1.19→46.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 74 589 4105
Biso mean--22.34 32.12 -
Num. residues----478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083536
X-RAY DIFFRACTIONf_angle_d0.9814841
X-RAY DIFFRACTIONf_chiral_restr0.107624
X-RAY DIFFRACTIONf_plane_restr0.006635
X-RAY DIFFRACTIONf_dihedral_angle_d6.531163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1903-1.20380.3452560.3352977103310
1.2038-1.2180.37411170.35142213233023
1.218-1.23280.35951730.33583509368235
1.2328-1.24840.33523260.30865958628460
1.2484-1.26480.29213910.29767410780175
1.2648-1.28220.31534310.28738461889285
1.2822-1.30050.27374610.26468938939990
1.3005-1.31990.25254950.2339414990996
1.3199-1.34050.2435070.210696071011497
1.3405-1.36250.22255120.196197101022298
1.3625-1.3860.19085140.184997871030199
1.386-1.41120.17515160.1698983210348100
1.4112-1.43840.18125240.1673987010394100
1.4384-1.46770.1585150.1548980410319100
1.4677-1.49960.1695110.1459987510386100
1.4996-1.53450.15555210.1394989010411100
1.5345-1.57290.17035220.1357983110353100
1.5729-1.61540.14145200.1352987810398100
1.6154-1.6630.1485190.1341985610375100
1.663-1.71660.16515180.1342988010398100
1.7166-1.7780.15545200.1293979310313100
1.778-1.84920.15915120.1289987610388100
1.8492-1.93340.14575200.1214983910359100
1.9334-2.03530.12455220.117998001032299
2.0353-2.16280.13585190.12398331035299
2.1628-2.32980.13825140.126398481036299
2.3298-2.56420.15885260.136798151034199
2.5642-2.93520.14655050.136797791028499
2.9352-3.69790.14815150.131198021031799
3.6979-46.95290.15565180.145297981031699
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)
14.13791.0979-1.12791.1391-0.75291.20650.0593-0.1050.15790.1213-0.0243-0.0515-0.10190.0323-0.02680.113-0.0129-0.00040.0988-0.00730.1419-7.6647-0.738933.8221
23.61170.83021.03261.64330.2211.2428-0.04320.12250.2106-0.0750.01190.1167-0.1447-0.00510.03670.09350.0096-0.0060.11950.0280.1064-15.1278-1.845122.6797
34.55453.05113.52082.92951.34863.9588-0.18680.21550.3657-0.20220.00740.0897-0.33750.01710.14640.13020.0189-0.00570.18760.03810.1775-13.92832.76519.4464
41.71350.1457-0.26491.065-0.05920.9719-0.05640.24440.0556-0.14350.02890.0737-0.0517-0.02970.02730.11210.0131-0.02130.13670.02660.1233-15.7464-6.754117.8464
55.63340.61971.3830.36860.3840.58020.0091-0.010.49090.0093-0.06130.0569-0.1696-0.00790.05030.1021-0.008-0.00520.11060.01790.1769-11.49732.985828.8999
60.5893-0.25750.56720.9537-0.37761.0964-0.02360.0217-0.03220.07040.04320.1485-0.0886-0.0944-0.00830.07690.00530.00830.09130.01190.1212-18.3182-7.24930.7853
70.1870.0855-0.38220.4865-0.30120.869-0.0190.0752-0.0751-0.0614-0.0112-0.0011-0.020.01520.02310.07530.0045-0.00630.09380.00920.1174-7.6192-8.473126.136
83.3187-0.35530.81641.3825-0.41651.9113-0.0485-0.0314-0.13940.06470.06290.10840.1143-0.111-0.06020.1025-0.0126-0.00280.1017-0.00980.1256-17.281-26.996330.0514
92.09280.9806-1.34391.3444-0.42141.4509-0.05840.37470.1233-0.13980.0904-0.0070.0417-0.05670.00070.10320.0153-0.00240.1372-0.00220.0977-8.8872-18.196819.3226
102.55110.8019-0.60190.9372-0.16741.5574-0.13680.2531-0.2797-0.14890.0832-0.03550.2417-0.07920.07320.15160.00230.00980.1697-0.04160.1671-11.039-27.932518.1848
113.17330.0979-0.55657.14673.48126.4066-0.06090.19540.1563-0.45880.0868-0.2584-0.32230.296-0.00630.1289-0.01380.01390.1920.02570.1390.0816-12.377916.1439
122.7481.3611-0.84391.3602-1.08112.244-0.12660.3783-0.1645-0.15620.14340.05520.1873-0.218-0.00970.11610.00880.00040.1495-0.03640.1381-17.8444-22.861619.2367
138.06191.9743-3.27251.0676-1.50382.1548-0.29280.1765-0.5657-0.1250.073-0.21210.2206-0.00380.20240.11340.00570.00780.135-0.03790.1722-8.5975-28.494923.5892
140.9959-0.537-0.25913.692.90852.32290.21370.537-0.2002-0.7562-0.1569-0.41140.49310.3280.0230.24630.06690.05310.2017-0.03870.18992.206-29.211820.0754
150.23670.1195-0.42610.5956-0.02431.03770.01780.002-0.00640.0274-0.018-0.04930.02440.06910.0160.08090.0071-0.00580.095-0.00380.1051-7.7389-18.398830.1882
160.06360.20690.17340.85510.1771.1325-0.01070.0470.2465-0.03530.00020.05530.0184-0.08650.03440.06840.0099-0.00710.1148-0.0070.1188-17.3854-17.437724.928
170.71570.2199-0.08484.60671.8662.50810.06140.02180.0650.05790.0451-0.2951-0.13550.2238-0.06530.1407-0.0263-0.03480.12750.0080.1481.5026-12.663844.0025
181.11940.33020.31441.2876-0.250.75750.1389-0.1091-0.14290.3-0.0956-0.19350.04330.0734-0.02740.2366-0.0366-0.06170.12850.02320.1165-3.0797-22.486655.1176
192.1152.195-0.99483.4251-1.04421.65230.1868-0.1906-0.01590.4299-0.2318-0.2839-0.1350.2154-0.01070.2434-0.052-0.06650.15870.0250.1457-0.9265-13.338455.2826
201.01791.5327-0.49133.544-1.95611.80060.0547-0.0289-0.15150.1008-0.1153-0.42170.09260.25140.08850.1849-0.0063-0.06120.13810.01170.16992.6502-22.396348.8985
216.08021.4246-0.85487.2346-3.05488.55360.0115-0.4546-0.43620.36280.1002-0.15710.50910.3810.03960.270.0313-0.08740.18990.02290.2342.144-33.622250.6565
220.71180.05770.27141.1658-0.92370.95670.1060.0123-0.07090.129-0.091-0.04050.06380.03650.00840.1282-0.0103-0.02130.1015-0.00150.1051-8.2521-20.935543.9398
230.8820.16520.20010.0423-0.07291.08310.1156-0.13010.04340.2619-0.12010.179-0.054-0.00460.01460.176-0.0279-0.01370.1054-0.00440.1056-7.0838-12.247850.5983
241.22770.19360.74793.9244-0.58342.30260.13890.0074-0.02040.1092-0.05190.24010.0427-0.155-0.0940.1211-0.0160.03090.1243-0.00710.1391-26.2091-18.187943.3033
251.45970.4426-0.00521.06070.7551.20880.1577-0.2210.1570.2736-0.13760.2181-0.0288-0.12160.02570.2387-0.04580.06720.1338-0.02620.1237-23.3679-13.12155.9063
263.2152-2.7318-2.88993.55913.69724.72690.1436-0.58040.29090.4058-0.0265-0.1153-0.09910.2686-0.13570.3108-0.09360.0340.2048-0.05190.1539-11.1005-5.244261.0096
270.73611.00491.03582.11771.17052.76410.1853-0.23150.08660.3681-0.24640.28320.2288-0.3166-0.00290.218-0.06360.04820.1736-0.02180.1262-23.6246-20.739554.3197
281.55671.68531.18393.99652.78413.30690.1298-0.11330.24850.0119-0.22910.3877-0.179-0.25770.09120.1977-0.01850.07060.1294-0.02760.1769-27.2557-10.244450.7505
292.90750.1060.2981.98530.48116.81880.1349-0.56620.26720.5538-0.07120.336-0.5103-0.35670.00840.3255-0.00060.15140.2378-0.05290.2641-26.67060.075355.5508
300.6091-0.4428-0.62271.25261.12562.10950.118-0.0140.08280.1371-0.0366-0.0835-0.0175-0.0357-0.03190.1073-0.01390.01490.0855-0.0050.1147-16.8375-15.649543.1737
310.87290.35170.00091.30580.54810.9840.1414-0.06080.10940.1796-0.0968-0.0265-0.1451-0.0101-0.03040.1852-0.02690.04510.1065-0.01330.1096-16.5417-9.780849.973
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 34 )A13 - 34
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 42 )A35 - 42
4X-RAY DIFFRACTION4chain 'A' and (resid 43 through 56 )A43 - 56
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 69 )A57 - 69
6X-RAY DIFFRACTION6chain 'A' and (resid 70 through 104 )A70 - 104
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 114 )A105 - 114
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 12 )B1 - 12
9X-RAY DIFFRACTION9chain 'B' and (resid 13 through 25 )B13 - 25
10X-RAY DIFFRACTION10chain 'B' and (resid 26 through 42 )B26 - 42
11X-RAY DIFFRACTION11chain 'B' and (resid 43 through 47 )B43 - 47
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 61 )B48 - 61
13X-RAY DIFFRACTION13chain 'B' and (resid 62 through 69 )B62 - 69
14X-RAY DIFFRACTION14chain 'B' and (resid 70 through 74 )B70 - 74
15X-RAY DIFFRACTION15chain 'B' and (resid 75 through 104 )B75 - 104
16X-RAY DIFFRACTION16chain 'B' and (resid 105 through 114 )B105 - 114
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 12 )C1 - 12
18X-RAY DIFFRACTION18chain 'C' and (resid 13 through 47 )C13 - 47
19X-RAY DIFFRACTION19chain 'C' and (resid 48 through 61 )C48 - 61
20X-RAY DIFFRACTION20chain 'C' and (resid 62 through 69 )C62 - 69
21X-RAY DIFFRACTION21chain 'C' and (resid 70 through 74 )C70 - 74
22X-RAY DIFFRACTION22chain 'C' and (resid 75 through 104 )C75 - 104
23X-RAY DIFFRACTION23chain 'C' and (resid 105 through 114 )C105 - 114
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 12 )D1 - 12
25X-RAY DIFFRACTION25chain 'D' and (resid 13 through 42 )D13 - 42
26X-RAY DIFFRACTION26chain 'D' and (resid 43 through 47 )D43 - 47
27X-RAY DIFFRACTION27chain 'D' and (resid 48 through 61 )D48 - 61
28X-RAY DIFFRACTION28chain 'D' and (resid 62 through 69 )D62 - 69
29X-RAY DIFFRACTION29chain 'D' and (resid 70 through 74 )D70 - 74
30X-RAY DIFFRACTION30chain 'D' and (resid 75 through 95 )D75 - 95
31X-RAY DIFFRACTION31chain '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