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- PDB-7k73: Structure of Enoyl-[acyl-carrier-protein] reductase [NADH] from M... -

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Basic information

Entry
Database: PDB / ID: 7k73
TitleStructure of Enoyl-[acyl-carrier-protein] reductase [NADH] from Mycobacterium fortuitum bound to NAD
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycolicibacterium fortuitum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Antimicrob.Agents Chemother. / Year: 2023
Title: In Vitro and In Vivo Efficacy of NITD-916 against Mycobacterium fortuitum.
Authors: Roquet-Baneres, F. / Alcaraz, M. / Hamela, C. / Abendroth, J. / Edwards, T.E. / Kremer, L.
History
DepositionSep 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / refine_ls_restr_ncs / struct_ncs_dom / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
E: Enoyl-[acyl-carrier-protein] reductase [NADH]
G: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,01320
Polymers117,6274
Non-polymers3,38616
Water22,4651247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21160 Å2
ΔGint-119 kcal/mol
Surface area33540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.940, 90.860, 91.910
Angle α, β, γ (deg.)90.000, 90.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADH]


Mass: 29406.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium fortuitum (bacteria)
Gene: fabI, inhA, A5637_21995, A5751_12770, FKW78_11710, NCTC1542_01491, XA26_29600
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0N9XSE6, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion
Details: MCSG-1 H3: 0.2 M Lithium Acetate, 20% (w/v) PEG 3350 + 5 mM NAD (BSI1606), 28.49 mg/mL MyfoA.00170.a.B1.PS38584 cryo: 20% EG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→38.85 Å / Num. obs: 112564 / % possible obs: 98.7 % / Redundancy: 3.811 % / Biso Wilson estimate: 24.641 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.058 / Χ2: 1.008 / Net I/σ(I): 18.24 / Num. measured all: 429032 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.853.4050.2684.3427645844281180.9360.31796.2
1.85-1.93.820.2235.6930783821680580.9620.2698.1
1.9-1.953.8650.1836.9930200794378130.9730.21398.4
1.95-2.013.8630.1548.3629306773175870.9810.17998.1
2.01-2.083.8570.12710.1128530750073970.9860.14798.6
2.08-2.153.8610.10411.8427651727271620.990.12198.5
2.15-2.233.8580.08514.3226575697468880.9930.09998.8
2.23-2.323.8610.07715.925724675866620.9940.08998.6
2.32-2.433.8540.06518.1924782648464310.9950.07699.2
2.43-2.553.8570.06219.2323623619261240.9950.07298.9
2.55-2.683.8560.05321.8922587590558570.9960.06299.2
2.68-2.853.8590.04724.221303556555200.9970.05499.2
2.85-3.043.8550.04127.2420007522051900.9970.04899.4
3.04-3.293.8390.03630.3618767491548890.9980.04299.5
3.29-3.63.8280.03333.7717145449344790.9980.03999.7
3.6-4.023.8210.02936.7215517408140610.9980.03499.5
4.02-4.653.8040.02839.2413688361135980.9980.03299.6
4.65-5.693.8010.02738.6611593306430500.9990.03299.5
5.69-8.053.7750.02838.118921237023630.9990.03299.7
8.05-38.853.5570.02840.84685135013170.9980.03397.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2h7i

2h7i
PDB Unreleased entry


Resolution: 1.8→38.85 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1766 1925 1.71 %
Rwork0.1461 110611 -
obs0.1466 112536 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.22 Å2 / Biso mean: 21.392 Å2 / Biso min: 7.92 Å2
Refinement stepCycle: final / Resolution: 1.8→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7780 0 224 1276 9280
Biso mean--18.5 30.74 -
Num. residues----1060
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.18661530.18167667782096
1.85-1.890.22291310.16827823795498
1.89-1.950.18881270.16187825795298
1.95-2.010.21811410.15527851799298
2.01-2.090.21031470.15317858800599
2.09-2.170.18911330.14577833796698
2.17-2.270.16381230.147953807699
2.27-2.390.19051440.14517839798399
2.39-2.540.19921530.15197899805299
2.54-2.730.17451390.15157966810599
2.73-3.010.1825990.14668011811099
3.01-3.440.1631040.144779998103100
3.44-4.340.14261850.128979908175100
4.34-38.850.17721460.14328097824399
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)
12.66130.53580.3472.9497-0.43671.7150.04510.241-0.0002-0.1993-0.09140.0888-0.0168-0.09290.08420.10090.0274-0.00660.1345-0.05060.074911.03033.3471-6.0811
22.05840.65420.54663.5404-1.16752.34450.04680.1656-0.4306-0.2356-0.02570.12060.2076-0.3612-0.00870.1294-0.0036-0.00640.203-0.10210.16426.442-6.5358-6.0822
31.3504-0.54790.68821.0223-0.1282.49660.01080.2134-0.1606-0.1066-0.15310.01750.2270.07950.0970.1082-0.0147-0.00540.1447-0.070.180511.3855-8.1322-3.5049
42.41350.126-1.11791.3422-0.78936.4047-0.01750.1092-0.3139-0.0003-0.0205-0.12620.37320.30880.08780.15040.0252-0.00010.1466-0.06750.237820.2736-13.2341-1.9588
50.63520.04170.10420.79790.26711.32610.0538-0.0179-0.08770.0319-0.06580.02110.1087-0.02790.00670.0848-0.0086-0.00090.0727-0.01640.127813.7773-1.536510.9769
60.98810.4996-0.0910.9591-0.09240.84330.0286-0.0313-0.10770.0692-0.0850.02840.0475-0.07830.05580.0927-0.00220.00090.0677-0.02080.104312.49653.344312.0046
73.23592.1367-0.70252.2836-0.75981.77990.0994-0.03580.19360.2171-0.09560.60670.0588-0.3438-0.04980.119-0.00160.02970.1979-0.04330.2632-3.675513.987510.5756
81.24880.03460.41530.7285-0.29620.7485-0.01160.08610.0015-0.0981-0.01860.0656-0.0353-0.04540.03770.10590.02640.01440.1238-0.01130.118518.45611.9794-0.6443
92.89310.86972.09033.4712-1.45824.29670.09570.07430.1480.1752-0.19270.1965-0.1555-0.3120.12670.0644-0.02270.02230.0655-0.0070.084810.425317.911112.8001
102.55930.3591-0.28312.86690.19821.8608-0.00090.29570.0359-0.2267-0.0897-0.07830.00940.0920.10260.1010.02140.00960.13740.05360.092126.353728.8908-6.1032
111.84860.4595-0.68543.06170.84372.1590.02780.21750.4337-0.1901-0.0111-0.1646-0.17920.3588-0.00330.13130.00350.01020.23480.1190.2231.295938.5209-6.2759
121.5788-0.9048-0.99911.3050.44213.693-0.0570.24650.2253-0.0944-0.1060.0065-0.0948-0.02940.14350.1145-0.0213-0.00180.15030.08490.211526.028240.3475-3.4718
132.88450.83141.93341.38391.85522.996-0.06960.08920.4535-0.0647-0.06350.1147-0.4462-0.23490.21230.16740.0297-0.01960.13670.08320.304917.114445.4293-1.8262
140.629-0.0330.07480.4591-0.07911.19090.00660.02370.12170.0076-0.0524-0.0144-0.11650.01020.06020.0923-0.00410.00020.0790.01970.154323.905433.64211.0599
150.69390.22170.24220.78970.10160.7979-0.01530.02420.10540.0399-0.0477-0.0635-0.07050.07340.06120.08570.0010.00270.06330.01780.107726.451428.687212.0923
163.62192.38261.02193.24860.57891.40850.05930.006-0.08990.2175-0.0733-0.41130.00910.2099-0.00540.11670.0165-0.00850.17440.0290.221940.192217.363610.2417
170.99510.5975-0.22141.2964-0.07661.60130.03070.07870.0536-0.0249-0.0711-0.02730.01950.03970.05130.0850.01280.00760.08480.00010.095322.146517.75594.7392
182.9977-0.20070.04652.58130.32781.33420.0362-0.38740.05110.4348-0.10940.1206-0.0169-0.18790.05550.2445-0.03850.01930.2397-0.07980.115116.133130.546748.5037
191.08210.4789-0.92861.302-0.7463.10070.0525-0.27890.29320.3451-0.06560.1213-0.4078-0.21010.00860.28690.0058-0.00680.2746-0.13110.202817.3341.142347.401
202.8822-1.06961.26893.958-3.24562.7696-0.0051-0.15510.32180.3759-0.1438-0.1638-0.59530.42610.17960.2942-0.0569-0.060.222-0.11070.273730.333343.007644.1645
210.3270.0426-0.12750.7875-0.06951.79610.0192-0.21530.11710.1535-0.092-0.1463-0.07360.11840.10310.1966-0.0324-0.02310.167-0.05260.176924.166734.876541.4766
220.94040.02810.63250.8148-0.41451.9897-0.0153-0.08570.17930.1238-0.0420.1074-0.2198-0.12380.07120.15310.00130.00190.1165-0.04980.192119.22738.870626.4629
230.61860.30370.74090.78620.23052.63740.0314-0.11020.11780.1295-0.09050.00950.0943-0.03260.00640.1623-0.01890.00970.1446-0.03310.131118.029526.552331.7695
241.3822-0.42740.29461.2673-0.38251.561-0.0455-0.15160.1660.0643-0.024-0.0525-0.0179-0.01280.07830.1369-0.0239-0.00250.0971-0.0250.119624.105328.851827.4064
251.80640.9992-0.70461.31580.34771.0665-0.1630.0920.45570.1935-0.0430.2102-0.2372-0.2810.17220.19730.0066-0.00180.201-0.04880.173912.458229.60634.5376
262.13560.9535-0.11415.7724-0.02384.9332-0.0838-0.10340.3796-0.2736-0.07870.9124-0.243-0.79520.15910.18310.02830.01020.326-0.08310.30050.457322.956633.6877
271.6352-0.19470.011.6512-0.08710.8541-0.0143-0.17760.02730.139-0.06070.10980.0207-0.09650.0760.1622-0.03880.02280.1426-0.01920.086616.292318.660137.6615
281.87550.4393-0.76991.7854-0.26551.42280.1538-0.3096-0.06870.4706-0.1168-0.13990.2094-0.09380.0110.3388-0.0763-0.01580.25510.06060.104722.03381.216348.3085
291.17520.94561.08271.5045-0.21272.56560.1417-0.2342-0.34990.4308-0.0779-0.16580.70260.0805-0.09250.4925-0.0445-0.02950.28730.12210.206123.0799-9.363348.1818
300.4081-0.1360.05590.1981-0.44831.20130.0638-0.2078-0.19120.3649-0.1087-0.00350.3867-0.1466-0.15370.4473-0.10830.00080.23160.08560.163617.8432-9.444145.6932
312.3232-0.3448-0.75741.50480.36135.966-0.0501-0.0703-0.22040.3483-0.13760.24050.5372-0.56570.13360.4334-0.17030.06430.32440.06060.26217.7884-11.207644.22
322.3377-1.1783-1.84251.06240.74464.256-0.0874-0.3662-0.30790.2446-0.04030.20860.3188-0.10020.26550.2417-0.1010.02870.21530.04710.164614.3607-2.865541.1257
334.861.56020.31834.0373-2.10543.48550.0704-0.2465-0.01080.0791-0.0801-0.4130.14290.395-0.01050.17390.0349-0.00540.1671-0.01670.261429.3968-8.37617.6642
341.1215-0.01640.1311.14820.13181.41970.0803-0.1966-0.09550.1909-0.1060.04270.1117-0.16360.020.1454-0.05430.0080.1280.02040.099715.32520.727429.9918
350.7315-0.36120.16630.8059-0.11760.384-0.04880.2018-0.31320.1449-0.0994-0.03790.29450.06080.15890.2403-0.00540.00970.18820.02380.176627.50580.861533.6384
361.7739-2.03270.31526.3196-0.04570.60270.04430.0152-0.275-0.2661-0.1162-0.97450.31070.2139-0.04080.233-0.00950.01370.20180.01850.272538.12578.512332.3728
371.4524-0.37750.41231.80930.25330.94290.0469-0.2217-0.02040.2123-0.0666-0.02070.0831-0.05670.01860.1534-0.0452-0.01070.1245-0.00080.07321.622713.252337.5932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )A2 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 53 )A32 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 67 )A54 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 82 )A68 - 82
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 158 )A83 - 158
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 207 )A159 - 207
7X-RAY DIFFRACTION7chain 'A' and (resid 208 through 235 )A208 - 235
8X-RAY DIFFRACTION8chain 'A' and (resid 236 through 255 )A236 - 255
9X-RAY DIFFRACTION9chain 'A' and (resid 256 through 269 )A256 - 269
10X-RAY DIFFRACTION10chain 'C' and (resid 2 through 31 )C2 - 31
11X-RAY DIFFRACTION11chain 'C' and (resid 32 through 53 )C32 - 53
12X-RAY DIFFRACTION12chain 'C' and (resid 54 through 67 )C54 - 67
13X-RAY DIFFRACTION13chain 'C' and (resid 68 through 82 )C68 - 82
14X-RAY DIFFRACTION14chain 'C' and (resid 83 through 158 )C83 - 158
15X-RAY DIFFRACTION15chain 'C' and (resid 159 through 209 )C159 - 209
16X-RAY DIFFRACTION16chain 'C' and (resid 210 through 235 )C210 - 235
17X-RAY DIFFRACTION17chain 'C' and (resid 236 through 269 )C236 - 269
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 31 )E2 - 31
19X-RAY DIFFRACTION19chain 'E' and (resid 32 through 67 )E32 - 67
20X-RAY DIFFRACTION20chain 'E' and (resid 68 through 82 )E68 - 82
21X-RAY DIFFRACTION21chain 'E' and (resid 83 through 99 )E83 - 99
22X-RAY DIFFRACTION22chain 'E' and (resid 100 through 137 )E100 - 137
23X-RAY DIFFRACTION23chain 'E' and (resid 138 through 158 )E138 - 158
24X-RAY DIFFRACTION24chain 'E' and (resid 159 through 182 )E159 - 182
25X-RAY DIFFRACTION25chain 'E' and (resid 183 through 213 )E183 - 213
26X-RAY DIFFRACTION26chain 'E' and (resid 214 through 235 )E214 - 235
27X-RAY DIFFRACTION27chain 'E' and (resid 236 through 269 )E236 - 269
28X-RAY DIFFRACTION28chain 'G' and (resid 2 through 31 )G2 - 31
29X-RAY DIFFRACTION29chain 'G' and (resid 32 through 53 )G32 - 53
30X-RAY DIFFRACTION30chain 'G' and (resid 54 through 67 )G54 - 67
31X-RAY DIFFRACTION31chain 'G' and (resid 68 through 82 )G68 - 82
32X-RAY DIFFRACTION32chain 'G' and (resid 83 through 99 )G83 - 99
33X-RAY DIFFRACTION33chain 'G' and (resid 100 through 112 )G100 - 112
34X-RAY DIFFRACTION34chain 'G' and (resid 113 through 182 )G113 - 182
35X-RAY DIFFRACTION35chain 'G' and (resid 183 through 210 )G183 - 210
36X-RAY DIFFRACTION36chain 'G' and (resid 211 through 235 )G211 - 235
37X-RAY DIFFRACTION37chain 'G' and (resid 236 through 269 )G236 - 269

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