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- PDB-6s7g: Cfucosylated linker peptide SBL1 bound to Fucose binding Lectin L... -

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Basic information

Entry
Database: PDB / ID: 6s7g
TitleCfucosylated linker peptide SBL1 bound to Fucose binding Lectin LecB (PA-IIL) from Pseudomonas aeruginosa at 1.84 Angstrom resolution
Components
  • Fucose-binding lectin
  • SBL1
KeywordsSUGAR BINDING PROTEIN / Lectin / Fucosylated
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 / molecular replacement / Resolution: 1.841 Å
AuthorsBaeriswyl, S. / Stocker, A. / Reymond, J.-L.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Helv.Chim.Acta / Year: 2019
Title: X-Ray Crystal Structure of a Second Generation Peptide Dendrimer in Complex with Pseudomonas aeruginosa Lectin LecB
Authors: Baeriswyl, S. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.-L.
History
DepositionJul 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fucose-binding lectin
B: Fucose-binding lectin
F: SBL1
C: Fucose-binding lectin
G: SBL1
D: Fucose-binding lectin
H: SBL1
E: SBL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,16320
Polymers49,0188
Non-polymers1,14512
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-145 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.230, 56.742, 70.622
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
11A-465-

HOH

21D-437-

HOH

31D-500-

HOH

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Components

#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 LecB from Pseudomonas aeruginosa (PA-IIL)
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: Protein/peptide
SBL1


Mass: 519.681 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Cfucosylated Linker peptide SBL1 / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.5 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.799998 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 28, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.799998 Å / Relative weight: 1
ReflectionResolution: 1.841→46.428 Å / Num. obs: 82590 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 23.4 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.286 / Net I/σ(I): 4.69
Reflection shellResolution: 1.841→1.85 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.77 / Num. unique obs: 13122 / CC1/2: 0.29 / Rrim(I) all: 1.58 / % possible all: 97.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.86 Å46.43 Å
Translation2.86 Å46.43 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OXC
Resolution: 1.841→46.428 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.17 / Phase error: 20.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 4093 4.96 %
Rwork0.1884 78434 -
obs0.1895 82527 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.63 Å2 / Biso mean: 23.8839 Å2 / Biso min: 8.4 Å2
Refinement stepCycle: final / Resolution: 1.841→46.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3394 0 90 458 3942
Biso mean--29.82 32.39 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033453
X-RAY DIFFRACTIONf_angle_d0.6014726
X-RAY DIFFRACTIONf_chiral_restr0.051605
X-RAY DIFFRACTIONf_plane_restr0.002626
X-RAY DIFFRACTIONf_dihedral_angle_d11.3261980
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.841-1.86220.31741350.3112258194
1.8622-1.88490.3221380.2991269699
1.8849-1.90870.34131400.3048263998
1.9087-1.93390.29591430.291271299
1.9339-1.96040.31851420.2869271799
1.9604-1.98840.28191390.26382672100
1.9884-2.0180.271440.25842734100
2.018-2.04960.25671410.2402267099
2.0496-2.08320.24721420.23732724100
2.0832-2.11910.23541400.22552720100
2.1191-2.15760.2551400.22342701100
2.1576-2.19910.23721420.21322722100
2.1991-2.2440.24021430.20772688100
2.244-2.29280.25641380.20372713100
2.2928-2.34610.23991420.1942721100
2.3461-2.40480.22881410.1972707100
2.4048-2.46980.2541440.19492729100
2.4698-2.54250.22521410.18542715100
2.5425-2.62460.22131450.18182720100
2.6246-2.71830.19281430.16932739100
2.7183-2.82720.18421410.16132726100
2.8272-2.95580.19091430.16062703100
2.9558-3.11160.17821400.14982709100
3.1116-3.30650.21370.14462723100
3.3065-3.56170.16061470.1332720100
3.5617-3.920.13881400.12862706100
3.92-4.48680.15381380.13652698100
4.4868-5.65140.15721420.15342730100
5.6514-46.4280.2061420.2432269999
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.24820.1551-0.61861.06080.12762.4392-0.0021-0.0473-0.170.1053-0.0146-0.20710.29390.13320.04430.18010.013-0.02480.14330.00510.207-11.79055.6805-16.3258
20.1353-0.0630.21430.3232-0.34085.9954-0.0044-0.1435-0.0528-0.02090.1245-0.074-0.04460.0449-0.1640.21830.04740.02270.2360.00410.2645-7.9354-1.2806-19.0522
33.7689-1.4688-4.47517.9032-0.53786.10990.14230.7027-0.3018-0.4344-0.0584-0.10130.147-0.4767-0.13440.2297-00.00010.2303-0.02550.1581-11.42476.0637-35.0316
41.58970.7646-1.73551.3931-0.72414.03970.0883-0.2654-0.1877-0.0067-0.1035-0.1850.18150.2470.00880.17190.0411-0.03140.14210.0070.1767-12.40932.6044-15.024
53.80320.17653.19233.2874.57598.6495-0.11090.5246-0.1284-0.8430.2045-0.3752-0.15180.8816-0.11940.23510.01160.08980.2930.00590.29641.74757.9641-24.8898
63.6716-1.5053-1.32441.43251.11611.16230.1930.07220.11440.0274-0.0828-0.0451-0.01720.0073-0.07840.1652-0.0043-0.00490.12820.01520.1311-18.438313.9021-16.2747
72.0355-0.2583-1.31350.8553-0.21542.12660.03660.01550.2642-0.08570.0657-0.09360.01990.1516-0.08290.1710.00030.00970.1375-0.02950.1793-13.077611.1966-23.0324
83.8278-0.05123.16240.86730.2814.5250.1429-0.0921-0.1564-0.0657-0.023-0.05430.2688-0.1679-0.06090.21710.00630.02930.1344-0.00240.1511-28.913519.3126-3.4248
91.8183-0.39091.10771.9656-1.82573.2298-0.09640.02690.16840.2216-0.01810.0457-0.27480.02730.16880.15790.01340.0080.1255-0.03840.1404-29.865934.949-7.6899
100.6992-1.1001-0.14888.9009-6.4196.27080.05650.0334-0.20980.45740.21950.5846-0.2712-0.041-0.2950.26420.01020.02520.1482-0.0240.1952-35.915828.4132-1.4274
110.66090.23390.20892.0556-1.74932.0722-0.1033-0.01380.0274-0.15460.0752-0.01170.0409-0.10350.03480.25910.00830.03080.1393-0.01820.1852-33.633237.7474-6.6789
122.9361-4.1444.47515.7143-6.146.5894-0.145-0.0778-0.02350.7316-0.03140.0634-0.494-0.12220.11670.2446-0.00420.03530.1562-0.02290.1418-26.93334.7613-1.313
132.4745-2.29923.03373.2993-3.44474.7477-0.2464-0.4717-0.1630.12890.40620.2667-0.232-0.602-0.2570.20320.03420.03020.19750.00660.1901-34.147724.2817-1.9447
141.9281-1.9886-2.37712.6513.26214.0401-0.45530.51410.91180.4632-0.32421.3443-0.1871-0.69430.55620.29770.03270.05920.1942-0.0530.4515-45.045832.5136-10.5821
154.2568-2.475-0.37012.51230.14270.5335-0.13630.1243-0.10280.20150.0970.0596-0.10270.07780.02670.1636-0.02120.01350.13430.00110.1205-24.693923.1855-11.3364
161.077-0.76750.74870.6691-0.67521.59630.19530.0089-0.1224-0.0966-0.07870.0630.1693-0.0436-0.12230.1697-0.0128-0.00570.1347-0.00170.1724-30.153930.3031-12.8002
176.78121.447-6.70280.8134-1.12757.660.02950.24480.03110.0271-0.1583-0.058-0.1041-0.23060.14120.1710.0196-0.02340.17090.0040.1542-28.197320.3411-30.8124
180.55210.5980.02362.3586-1.39362.4828-0.00740.073-0.0331-0.17870.0520.00980.2226-0.0794-0.05090.19470.0239-0.00020.1302-0.01190.1372-30.70536.7263-30.692
195.64753.6248-0.40114.04892.16243.8743-0.2697-0.1882-0.00420.106-0.1018-0.0156-0.0068-0.17850.29870.24280.007-0.04870.18240.020.1762-28.7511-3.6617-19.3963
200.45580.46060.15351.9139-1.21841.5426-0.08580.07910.0545-0.14850.1343-0.02430.094-0.0981-0.05720.2026-0.0038-0.00780.1636-0.02620.1389-28.563611.1609-33.13
213.5579-2.48723.5783.16840.1048.45840.4152-0.0725-0.5264-0.426-0.511.44320.502-0.48110.12630.1909-0.0255-0.05860.1593-0.0350.3145-42.57944.6632-24.344
220.1761-0.0267-0.06250.52440.60630.4903-0.0041-0.03340.07380.01010.01080.038-0.0196-0.0255-0.0040.17580.0183-0.00290.15770.01080.1471-26.167213.1955-22.1481
236.6639-3.10652.84952.0028-1.45952.190.16460.38010.1053-0.2352-0.2324-0.13860.16710.21880.04420.1665-0.0012-0.00460.15280.02190.1634-15.134131.5458-24.8805
241.92180.03381.74870.7463-0.97485.3136-0.05220.03790.21820.0177-0.0325-0.0305-0.18910.26660.08590.2091-0.0150.01250.1197-0.02540.1851-13.111138.0597-13.3054
250.9193-0.0947-0.92770.731-1.17156.09810.0831-0.01520.1477-0.07530.0984-0.0717-0.07720.185-0.00530.2476-0.0352-0.00710.1838-0.0160.2017-11.01443.2205-14.7273
269.1165.53756.62663.44453.85225.12960.3235-0.42940.41850.6160.05440.11690.1298-0.2687-0.25130.22-0.00360.05680.1611-0.06320.2492-14.705835.99191.2502
270.68270.33990.72260.6620.14322.2368-0.0550.0840.10330.0135-0.04880.0111-0.09730.15290.1270.2205-0.01080.02010.14650.02360.1885-14.763938.7225-18.741
284.63083.8946-2.61964.0663-1.07623.08530.0195-0.09370.06180.50020.3311-0.3193-0.66510.2723-0.35840.2065-0.0197-0.01330.2087-0.01360.1973-0.767635.3912-8.4129
292.89741.13211.57050.44150.90641.40940.0855-0.1204-0.0562-0.1001-0.0521-0.03830.0327-0.0767-0.00140.1609-0.00680.01040.15310.01320.1467-19.362126.8865-17.4067
301.4-0.10950.30540.0082-0.01560.50760.1509-0.05930.0421-0.0405-0.06480.00180.08680.0474-0.0720.1887-0.02730.00460.1541-0.00010.1563-14.814630.4129-10.3756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 34 )A1 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 42 )A35 - 42
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 47 )A43 - 47
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 68 )A48 - 68
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 74 )A69 - 74
6X-RAY DIFFRACTION6chain 'A' and (resid 75 through 95 )A75 - 95
7X-RAY DIFFRACTION7chain 'A' and (resid 96 through 114 )A96 - 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 34 )B26 - 34
11X-RAY DIFFRACTION11chain 'B' and (resid 35 through 47 )B35 - 47
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 56 )B48 - 56
13X-RAY DIFFRACTION13chain 'B' and (resid 57 through 69 )B57 - 69
14X-RAY DIFFRACTION14chain 'B' and (resid 70 through 74 )B70 - 74
15X-RAY DIFFRACTION15chain 'B' and (resid 75 through 95 )B75 - 95
16X-RAY DIFFRACTION16chain 'B' and (resid 96 through 114 )B96 - 114
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 12 )C1 - 12
18X-RAY DIFFRACTION18chain 'C' and (resid 13 through 42 )C13 - 42
19X-RAY DIFFRACTION19chain 'C' and (resid 43 through 47 )C43 - 47
20X-RAY DIFFRACTION20chain 'C' and (resid 48 through 68 )C48 - 68
21X-RAY DIFFRACTION21chain 'C' and (resid 69 through 74 )C69 - 74
22X-RAY DIFFRACTION22chain 'C' and (resid 75 through 114 )C75 - 114
23X-RAY DIFFRACTION23chain 'D' and (resid 1 through 12 )D1 - 12
24X-RAY DIFFRACTION24chain 'D' and (resid 13 through 34 )D13 - 34
25X-RAY DIFFRACTION25chain 'D' and (resid 35 through 42 )D35 - 42
26X-RAY DIFFRACTION26chain 'D' and (resid 43 through 47 )D43 - 47
27X-RAY DIFFRACTION27chain 'D' and (resid 48 through 68 )D48 - 68
28X-RAY DIFFRACTION28chain 'D' and (resid 69 through 74 )D69 - 74
29X-RAY DIFFRACTION29chain 'D' and (resid 75 through 95 )D75 - 95
30X-RAY DIFFRACTION30chain 'D' and (resid 96 through 114 )D96 - 114

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  • 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

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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

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