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- PDB-6yua: CO-dehydrogenase coupled to the N-terminal domain of the Acetyl-C... -

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Basic information

Entry
Database: PDB / ID: 6yua
TitleCO-dehydrogenase coupled to the N-terminal domain of the Acetyl-CoA synthase from Clostridium autoethanogenum isolated after tryptic digestion.
Components
  • CO dehydrogenase/acetyl-CoA synthase complex, beta subunit
  • Carbon-monoxide dehydrogenase (Acceptor),CO-dehydrogenase from Clostridium autoethanogenum DSM 10061
KeywordsOXIDOREDUCTASE / C1-Metabolism / Carbon monoxide / metalloprotein / Acetogenic bacteria / Acetogenesis / CO-dehydrogenase/Acetyl-CoA synthase / X-ray crystal structure / Gas channeling / Waste-gas conversion.
Function / homology
Function and homology information


carbon-monoxide dehydrogenase (acceptor) / CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / : / acetyl-CoA metabolic process / nickel cation binding / generation of precursor metabolites and energy / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / ACS/CODH beta subunit C-terminal / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family ...CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / Carbon monoxide dehydrogenase subunit alpha ,N-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / ACS/CODH beta subunit C-terminal / CO dehydrogenase, alpha-bundle / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / Carbon-monoxide dehydrogenase (Acceptor) / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesClostridium autoethanogenum DSM 10061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.16 Å
AuthorsWagner, T. / Lemaire, O.N.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)DFG-SPP 1927 WA 4053/1-1 Germany
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum.
Authors: Lemaire, O.N. / Wagner, T.
History
DepositionApr 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CO dehydrogenase/acetyl-CoA synthase complex, beta subunit
B: Carbon-monoxide dehydrogenase (Acceptor),CO-dehydrogenase from Clostridium autoethanogenum DSM 10061
C: Carbon-monoxide dehydrogenase (Acceptor),CO-dehydrogenase from Clostridium autoethanogenum DSM 10061
D: CO dehydrogenase/acetyl-CoA synthase complex, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,63016
Polymers201,4114
Non-polymers2,21912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14410 Å2
ΔGint-209 kcal/mol
Surface area61990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.333, 89.333, 527.130
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain D and resid 1 through 290)
12chain B
22(chain C and resid 3 through 631)

NCS domain segments:

Component-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETchain AAA1 - 2901 - 290
21METMET(chain D and resid 1 through 290)DD1 - 2901 - 290
12GLUGLUchain BBB3 - 6313 - 631
22GLUGLU(chain C and resid 3 through 631)CC3 - 6313 - 631

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ADBC

#1: Protein CO dehydrogenase/acetyl-CoA synthase complex, beta subunit


Mass: 32728.072 Da / Num. of mol.: 2 / Mutation: wild-type / Source method: isolated from a natural source
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: /
References: UniProt: U5RWA4, CO-methylating acetyl-CoA synthase
#2: Protein Carbon-monoxide dehydrogenase (Acceptor),CO-dehydrogenase from Clostridium autoethanogenum DSM 10061


Mass: 67977.531 Da / Num. of mol.: 2 / Mutation: wild-type / Source method: isolated from a natural source
Details: A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401). ...Details: A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401).,A stop codon is present in the gene and the CODH seems to be split in two peptides. However, experimental evidence proved that a stop codon read-through occurs leading to a cysteine (C401).
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
Cell line: / / Organ: / / Plasmid details: / / Variant: / / Tissue: /
References: UniProt: U5RTE2, carbon-monoxide dehydrogenase (acceptor), anaerobic carbon monoxide dehydrogenase

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Non-polymers , 5 types, 12 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2

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Details

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: 2.61 Å3/Da / Density % sol: 52.98 % / Description: Brown brick shape
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Crystallization was performed in an anoxic chamber (N2/H2, 95:5 %) with anaerobic solutions. Crystals were obtained by initial screening at 291.15 K using the sitting drop method on a 96- ...Details: Crystallization was performed in an anoxic chamber (N2/H2, 95:5 %) with anaerobic solutions. Crystals were obtained by initial screening at 291.15 K using the sitting drop method on a 96-well MRC 2 Crystallization Plates in polystyrene (SWISSCI). The crystallization reservoir contained 90 uL of mother liquor, crystallization drop contained a mixture of 0.6 uL protein and 0.6 uL precipitant. The protein concentration was 28.5 mg/mL in 25 mM Tris pH 7.6, 10% (v/v) glycerol and 2 mM dithiothreitol. The best diffracting crystal of CODH bound to the ACS N-terminal domain was obtained by initial screening using the Shotgun (SG1) screen from Molecular dimensions. The crystallization reservoir contained 200 mM Magnesium chloride hexahydrate and 20% (w/v) polyethylene glycol 3350. The crystal was cryoprotected in the same crystallization solution supplemented with 25% ethylene glycol.
PH range: / / Temp details: fluctuation of 1K

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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: Dec 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→131.783 Å / Num. obs: 17564 / % possible obs: 84.3 % / Redundancy: 17.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.061 / Rrim(I) all: 0.268 / Net I/σ(I): 8.9
Reflection shellResolution: 3.14→3.576 Å / Redundancy: 23.6 % / Rmerge(I) obs: 1.492 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 977 / CC1/2: 0.748 / Rpim(I) all: 0.309 / Rrim(I) all: 1.524 / % possible all: 81.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YTT

6ytt


Resolution: 3.16→39.95 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 893 5.1 %
Rwork0.2238 16633 -
obs0.2252 17526 45.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.7 Å2 / Biso mean: 65.4363 Å2 / Biso min: 12.21 Å2
Refinement stepCycle: final / Resolution: 3.16→39.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13810 0 62 0 13872
Biso mean--84.61 --
Num. residues----1848
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2655X-RAY DIFFRACTION5.11TORSIONAL
12D2655X-RAY DIFFRACTION5.11TORSIONAL
21B5881X-RAY DIFFRACTION5.11TORSIONAL
22C5881X-RAY DIFFRACTION5.11TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.16-3.360.295130.32422632764
3.36-3.620.2551390.299683687514
3.62-3.980.285680.27921428149624
3.98-4.550.26681670.23312994316150
4.55-5.730.27052530.23374790504379
5.73-39.950.23363530.20236322667598
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)
11.4708-0.0642-0.57192.02850.40792.4547-0.2461-0.3595-0.36510.01180.3433-0.06240.4940.22240.00940.30961.0172-0.178-0.59730.75510.2184-9.15186.731519.5677
21.0677-1.52930.96542.2038-2.15463.75690.1605-0.4199-0.23480.4362-0.4995-0.179-0.25650.23630.00011.3496-0.26420.20291.2532-0.1663-0.0578-11.556622.088231.2248
30.89950.18350.44451.6515-0.23931.6944-0.1053-0.5288-0.08260.21760.0061-0.1925-0.5425-0.4740.05150.48610.10260.17670.5726-0.03140.2466-7.001119.264821.9441
44.52911.5355-0.24270.68840.10353.68910.5602-0.2676-0.6170.3004-0.5729-0.7574-0.49860.6583-0.16670.4151-0.12680.00040.5081-0.10940.567512.542322.800312.6036
55.5557-0.5396-1.27280.76480.78673.28810.1598-0.34640.2827-0.35430.1814-0.5336-0.22850.2002-0.08820.631-0.18840.08570.7576-0.20190.202412.765824.584820.676
60.29090.55920.16142.04071.14651.02750.9245-0.04061.1360.7460.4980.5993-0.4047-1.36850.13220.1149-0.4531-0.22050.4196-0.76380.5075-8.951329.0317.8856
73.11950.722-0.16133.0659-0.61861.9268-0.04830.36150.00980.1205-0.6218-0.3617-0.26030.52930.54960.6025-0.12570.03770.62760.10520.33922.051921.09614.4789
80.0225-0.0614-0.11330.87190.95650.68390.1229-0.3965-0.28860.09950.09970.09210.1757-0.2588-0.05830.79170.77370.12861.5374-0.15420.8809-45.65317.0366-29.6869
90.7147-0.2655-0.01730.48650.51551.15960.183-0.40240.11620.5691-0.09190.4395-0.0836-0.2069-0.02330.31750.2110.01650.66050.05590.3493-30.58682.3452-38.108
103.83510.591-0.49872.32031.77961.72720.3514-0.23250.35080.57190.0963-0.14980.0640.9623-0.27570.8360.17690.12640.75870.12290.4389-1.55126.6625-38.456
111.23450.4632-0.56742.58480.2231.2349-0.24570.2308-0.0594-0.57310.4729-0.0435-0.54260.85380.00750.06430.29490.04570.4057-0.08040.4084-6.99228.9524-36.8313
120.5809-0.56170.2080.4325-0.23790.45120.5463-0.22160.17420.1542-0.592-0.0312-0.92350.4023-0.00820.23560.65640.12250.0330.18740.549-21.701316.4209-34.164
131.7931-0.2358-0.25940.7560.47673.28470.1780.36170.0831-0.26670.00010.3361-0.858-0.1118-0.22250.85580.41760.11190.78640.11140.5437-30.171234.0112-37.3402
140.34710.09760.31830.4425-0.39591.22390.3417-0.12060.34030.1719-0.20380.1313-0.9292-0.39460.00130.70480.49260.10180.50320.02220.4281-22.118326.5761-18.1676
150.61690.7458-0.37570.8370.29770.9270.5192-0.1291-0.60730.2844-0.02890.10170.0337-0.4803-0.08290.36330.21630.17830.46960.03620.2694-22.21625.6561-19.756
161.10641.35410.62681.87811.57771.9273-0.3652-0.54730.5846-0.23890.16640.70080.1845-0.79390.11210.56620.31810.06040.80990.06510.7399-44.8783-11.6152-47.8507
171.23780.70480.53261.1567-0.74191.1338-0.6713-0.2589-0.38380.14880.73860.4308-0.2333-0.1191-0.09570.32440.2183-0.04620.25480.33130.4099-34.31718.0801-47.6007
182.43550.9594-1.0111.74051.05162.1319-0.1293-0.162-0.2774-0.0244-0.1077-0.8853-0.59470.43760.01580.39150.20850.21880.65290.09590.7809-3.07-3.2755-65.2047
191.1550.56380.27391.7150.23640.61830.0430.1245-0.1423-0.33720.1117-0.33410.10420.263-0.16230.48590.1191-0.04140.3598-0.0380.3145-20.73412.8038-58.7064
201.0336-0.4533-0.12991.3851-0.23051.5255-0.3519-0.2811-0.42770.15490.1903-0.1680.39060.24690.17450.46350.026-0.00880.47630.10080.473-25.2405-17.489-60.081
210.97620.0085-0.60181.356-1.25141.405-0.3436-0.2468-0.3152-0.03730.6888-0.09890.42350.136-0.02550.5950.0892-0.0368-0.02950.0410.4683-33.1311-11.9911-76.2989
221.0361-0.1603-0.3930.99780.23351.54260.18730.35810.0085-0.07290.0773-0.0332-0.8365-0.40520.01630.15360.0205-0.12130.25270.05730.3356-36.60566.2499-67.46
230.4211-0.18140.56170.35820.48454.3411-0.27430.23960.6984-0.76970.26790.4716-0.3512-0.38930.26260.8628-0.0792-0.44780.7403-0.04940.5128-48.01426.3438-106.9475
240.29710.34020.29520.67310.4871.33570.8440.64380.4846-0.5521-0.5169-0.0651-0.276-0.19990.02530.8587-0.1893-0.29270.6206-0.23160.4786-51.0651-6.4403-111.1429
252.16590.11630.83821.33340.44930.41990.41810.59980.0482-0.8911-0.27041.03760.1969-0.2653-0.24710.942-0.36820.0207-0.58710.24470.4116-44.805-1.7002-108.3084
264.8829-1.79141.58143.4192-0.08583.8293-0.0761.0078-0.0022-0.6646-0.5514-0.1904-0.2525-0.28740.32970.8271-0.05990.15390.6753-0.00330.325-32.6759-10.342-120.4755
271.6618-0.0607-0.61270.9597-0.3111.1208-0.02720.8366-0.2929-0.87190.0786-0.3661-0.95810.26490.0311.02-0.38120.3480.8515-0.02760.4638-26.3748-1.1358-116.1869
281.86891.5866-0.51342.33920.34620.57220.1429-0.0935-0.35630.1507-0.1496-0.04540.4279-0.1069-0.16510.5901-0.0651-0.17670.37810.0530.5622-35.3433-8.2264-104.2536
291.1186-0.39250.23120.90420.6710.97920.2174-0.08660.2431-0.32050.5217-0.8726-0.07640.9229-0.09770.5791-0.35440.10280.4593-0.38940.2643-22.59290.8702-100.243
304.3188-2.1151-1.23691.27180.59750.3376-0.3643-0.3467-1.17550.4310.0811-1.33030.31770.360.05920.8434-0.1926-0.0270.7083-0.02240.8725-11.1681-21.1319-108.687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 29 )A1 - 29
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 57 )A30 - 57
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 129 )A58 - 129
4X-RAY DIFFRACTION4chain 'A' and (resid 130 through 174 )A130 - 174
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 191 )A175 - 191
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 226 )A192 - 226
7X-RAY DIFFRACTION7chain 'A' and (resid 227 through 290 )A227 - 290
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 53 )B3 - 53
9X-RAY DIFFRACTION9chain 'B' and (resid 54 through 105 )B54 - 105
10X-RAY DIFFRACTION10chain 'B' and (resid 106 through 136 )B106 - 136
11X-RAY DIFFRACTION11chain 'B' and (resid 137 through 182 )B137 - 182
12X-RAY DIFFRACTION12chain 'B' and (resid 183 through 260 )B183 - 260
13X-RAY DIFFRACTION13chain 'B' and (resid 261 through 370 )B261 - 370
14X-RAY DIFFRACTION14chain 'B' and (resid 371 through 523 )B371 - 523
15X-RAY DIFFRACTION15chain 'B' and (resid 524 through 631 )B524 - 631
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 54 )C3 - 54
17X-RAY DIFFRACTION17chain 'C' and (resid 55 through 105 )C55 - 105
18X-RAY DIFFRACTION18chain 'C' and (resid 106 through 136 )C106 - 136
19X-RAY DIFFRACTION19chain 'C' and (resid 137 through 260 )C137 - 260
20X-RAY DIFFRACTION20chain 'C' and (resid 261 through 472 )C261 - 472
21X-RAY DIFFRACTION21chain 'C' and (resid 473 through 523 )C473 - 523
22X-RAY DIFFRACTION22chain 'C' and (resid 524 through 631 )C524 - 631
23X-RAY DIFFRACTION23chain 'D' and (resid 1 through 29 )D1 - 29
24X-RAY DIFFRACTION24chain 'D' and (resid 30 through 77 )D30 - 77
25X-RAY DIFFRACTION25chain 'D' and (resid 78 through 102 )D78 - 102
26X-RAY DIFFRACTION26chain 'D' and (resid 103 through 134 )D103 - 134
27X-RAY DIFFRACTION27chain 'D' and (resid 135 through 208 )D135 - 208
28X-RAY DIFFRACTION28chain 'D' and (resid 209 through 252 )D209 - 252
29X-RAY DIFFRACTION29chain 'D' and (resid 253 through 285 )D253 - 285
30X-RAY DIFFRACTION30chain 'D' and (resid 286 through 300 )D286 - 300

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  • 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

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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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