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- PDB-5vl9: Crystal structure of EilR in complex with eilO DNA element -

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Basic information

Entry
Database: PDB / ID: 5vl9
TitleCrystal structure of EilR in complex with eilO DNA element
Components
  • DNA (5'-D(*GP*AP*AP*AP*GP*TP*TP*GP*GP*AP*CP*AP*TP*A)-3')
  • DNA (5'-D(*TP*AP*TP*GP*TP*CP*CP*AP*AP*CP*TP*TP*TP*C)-3')
  • Regulatory protein TetR
KeywordsTRANSCRIPTION/DNA / transcription factor / protein-DNA complex / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of biosynthetic process / regulation of primary metabolic process / DNA binding
Similarity search - Function
Tetracyclin repressor-like, C-terminal domain superfamily / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / DNA / DNA (> 10) / EilR repressor
Similarity search - Component
Biological speciesEnterobacter lignolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsPereira, J.H. / Ruegg, T.L. / Chen, J. / Novichkov, P. / DeGiovani, A. / Tomaleri, G.P. / Singer, S. / Simmons, B. / Thelen, M. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: Nat Commun / Year: 2018
Title: Jungle Express is a versatile repressor system for tight transcriptional control.
Authors: Ruegg, T.L. / Pereira, J.H. / Chen, J.C. / DeGiovanni, A. / Novichkov, P. / Mutalik, V.K. / Tomaleri, G.P. / Singer, S.W. / Hillson, N.J. / Simmons, B.A. / Adams, P.D. / Thelen, M.P.
History
DepositionApr 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 26, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulatory protein TetR
B: Regulatory protein TetR
C: Regulatory protein TetR
D: Regulatory protein TetR
E: DNA (5'-D(*TP*AP*TP*GP*TP*CP*CP*AP*AP*CP*TP*TP*TP*C)-3')
F: DNA (5'-D(*GP*AP*AP*AP*GP*TP*TP*GP*GP*AP*CP*AP*TP*A)-3')
G: DNA (5'-D(*TP*AP*TP*GP*TP*CP*CP*AP*AP*CP*TP*TP*TP*C)-3')
H: DNA (5'-D(*GP*AP*AP*AP*GP*TP*TP*GP*GP*AP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,52117
Polymers105,4578
Non-polymers1,0649
Water4,792266
1
A: Regulatory protein TetR
B: Regulatory protein TetR
E: DNA (5'-D(*TP*AP*TP*GP*TP*CP*CP*AP*AP*CP*TP*TP*TP*C)-3')
F: DNA (5'-D(*GP*AP*AP*AP*GP*TP*TP*GP*GP*AP*CP*AP*TP*A)-3')
G: DNA (5'-D(*TP*AP*TP*GP*TP*CP*CP*AP*AP*CP*TP*TP*TP*C)-3')
H: DNA (5'-D(*GP*AP*AP*AP*GP*TP*TP*GP*GP*AP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,87811
Polymers61,2876
Non-polymers5915
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Regulatory protein TetR
D: Regulatory protein TetR
E: DNA (5'-D(*TP*AP*TP*GP*TP*CP*CP*AP*AP*CP*TP*TP*TP*C)-3')
F: DNA (5'-D(*GP*AP*AP*AP*GP*TP*TP*GP*GP*AP*CP*AP*TP*A)-3')
G: DNA (5'-D(*TP*AP*TP*GP*TP*CP*CP*AP*AP*CP*TP*TP*TP*C)-3')
H: DNA (5'-D(*GP*AP*AP*AP*GP*TP*TP*GP*GP*AP*CP*AP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,76010
Polymers61,2876
Non-polymers4734
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.790, 74.060, 81.360
Angle α, β, γ (deg.)116.80, 105.19, 90.78
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Regulatory protein TetR


Mass: 22084.943 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter lignolyticus (bacteria) / Gene: Entcl_2353 / Production host: Escherichia coli (E. coli) / References: UniProt: E3G817
#2: DNA chain DNA (5'-D(*TP*AP*TP*GP*TP*CP*CP*AP*AP*CP*TP*TP*TP*C)-3')


Mass: 4205.752 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacter lignolyticus (bacteria)
#3: DNA chain DNA (5'-D(*GP*AP*AP*AP*GP*TP*TP*GP*GP*AP*CP*AP*TP*A)-3')


Mass: 4352.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacter lignolyticus (bacteria)
#4: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C6H14O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Lithium sulphate, 0.1 M Magnesium chloride, 0.1 M Hepes pH 7.5, 20 %PEG 3,350 and 10 % Hexanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.97965 Å
DetectorType: ADSC QUANTUM 315r / Detector: AREA DETECTOR / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.16→65.29 Å / Num. obs: 55872 / % possible obs: 95.7 % / Redundancy: 3.2 % / CC1/2: 0.995 / Net I/σ(I): 8.5

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Processing

Software
NameVersionClassification
PHENIX(dev_2650: ???)refinement
xia2data reduction
xia2data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.16→65.288 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 2854 5.11 %
Rwork0.194 --
obs0.1958 55872 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.16→65.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6020 1136 72 266 7494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027465
X-RAY DIFFRACTIONf_angle_d0.46710289
X-RAY DIFFRACTIONf_dihedral_angle_d14.1514246
X-RAY DIFFRACTIONf_chiral_restr0.0331136
X-RAY DIFFRACTIONf_plane_restr0.0011133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.19730.36591120.30922724X-RAY DIFFRACTION96
2.1973-2.23720.34531490.30092621X-RAY DIFFRACTION96
2.2372-2.28020.28821450.28522673X-RAY DIFFRACTION96
2.2802-2.32680.33121180.2692673X-RAY DIFFRACTION96
2.3268-2.37740.32471200.25732704X-RAY DIFFRACTION96
2.3774-2.43270.33111520.25682596X-RAY DIFFRACTION95
2.4327-2.49350.34411560.24622682X-RAY DIFFRACTION96
2.4935-2.56090.25891550.24042659X-RAY DIFFRACTION96
2.5609-2.63630.27321470.23322662X-RAY DIFFRACTION96
2.6363-2.72140.25781480.2322668X-RAY DIFFRACTION97
2.7214-2.81870.26971560.22592650X-RAY DIFFRACTION96
2.8187-2.93150.22531440.22252664X-RAY DIFFRACTION96
2.9315-3.06490.24941400.21652695X-RAY DIFFRACTION97
3.0649-3.22650.24171430.20922662X-RAY DIFFRACTION96
3.2265-3.42870.23031100.18962685X-RAY DIFFRACTION96
3.4287-3.69340.18821700.16772642X-RAY DIFFRACTION96
3.6934-4.0650.20441920.16112582X-RAY DIFFRACTION95
4.065-4.65310.19641510.14632571X-RAY DIFFRACTION94
4.6531-5.86180.18831340.1672565X-RAY DIFFRACTION92
5.8618-65.31810.1851120.15342640X-RAY DIFFRACTION94
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)
16.3864-4.25364.78455.8047-5.24859.1713-0.1895-0.4320.5483-0.36930.235-0.1263-0.4086-0.6020.04820.30040.02080.03730.35630.0550.3609-12.099-66.6289-0.3522
23.63190.46492.23121.8645-0.22232.50630.0718-0.07220.1716-0.0657-0.068-0.0993-0.0305-0.24310.02430.31990.02730.08170.35050.03970.3119-5.4225-69.662-0.2027
39.24150.7814-3.19086.0114.80489.0835-0.2793-0.6092-0.29320.20540.1385-0.0209-0.1126-0.13450.29790.45160.1350.05570.4510.01870.2944.4516-65.96125.2032
42.8581-0.66471.7254.65031.75964.9193-0.0922-0.13730.22620.22120.2551-0.0195-0.2985-0.3215-0.12050.23960.0390.00260.25790.00460.32897.4061-68.32599.5138
53.3185-2.118-0.10845.45820.93673.9375-0.2053-0.33860.45130.23770.1318-0.4953-0.4972-0.08180.10180.30020.0453-0.05870.2031-0.07350.370116.6881-67.350418.764
65.29973.29872.04888.29952.02356.6273-0.0575-0.3338-0.5070.16940.2966-0.50040.0619-0.7057-0.33650.31030.04150.04850.41010.04760.398115.8336-75.456625.1894
76.25610.0315-1.09348.68032.60985.2728-0.03550.4325-0.7137-0.52640.0673-0.42850.90340.1270.0530.62350.0905-0.01210.5031-0.02020.317928.36-99.1744-7.0737
87.82965.7566.24297.48756.41827.56070.44860.12-0.03060.4596-0.3169-0.01860.79230.1738-0.1370.41870.06880.04650.34870.04520.256530.1057-90.6324.238
96.14492.301-0.19432.79691.34873.719-0.52860.0238-1.2037-0.4495-0.7231-1.94480.30422.55261.03430.65650.03950.23430.64160.0411.090643.7437-77.321914.4958
104.13523.5511.75674.13080.17727.34850.43310.24850.32130.1113-0.1773-0.4539-0.2093-0.0947-0.16560.31610.04640.0940.30880.05830.49235.6307-75.071614.381
119.49324.8457-1.83173.4847-0.53753.44810.42510.55030.8163-0.1661-0.19160.3921-0.1652-0.0085-0.26380.35320.03270.02360.34620.03820.396223.2534-82.83861.506
127.19645.52095.3845.92694.86494.4416-0.00660.1351-0.11620.16970.1327-0.0550.37460.2109-0.19430.31790.03140.06690.27520.04190.325726.4059-86.61815.8288
137.6936-1.86885.81332.7359-1.87258.2843-0.2072-0.31770.10950.2206-0.02020.0402-0.3363-0.27630.270.30190.04280.05330.2373-0.01940.280725.5402-76.050320.2357
143.8089-1.06593.76385.8441-0.37613.7851-0.66160.83371.23970.8560.2914-0.1562-1.7621-1.71420.79210.87130.1237-0.06260.77680.10360.641319.7406-64.59484.0911
154.9663-4.06736.683.1602-4.39962.0821-0.35420.30080.7459-0.1044-0.4491-0.7151-0.41210.31850.5830.34880.00390.01510.37750.04120.468229.0295-67.811417.9712
166.0013-2.94361.41533.4322-4.09337.0812-0.1759-0.363-0.1847-0.22190.1959-0.09420.6168-0.2127-0.12740.4748-0.0325-0.0330.42620.01470.420513.1862-100.2332-31.4194
171.3586-0.3038-0.89982.7467-3.25337.6430.084-0.04480.0939-0.2395-0.0573-0.0159-0.03160.02830.00790.42170.0729-0.01950.3193-0.02260.368318.5067-91.3527-42.9216
186.2812-1.02070.30489.64627.05758.4405-0.2902-0.03560.0014-0.1987-0.16270.8327-0.5513-0.45480.45860.52210.0930.02140.35960.11430.41659.9218-84.5373-40.662
194.8278-0.8928-1.58342.988-0.62563.24990.35760.22020.4016-0.1634-0.2363-0.37850.17530.2172-0.13480.39250.0699-0.00720.30320.03560.459420.3244-77.1153-49.3988
206.23570.05994.4324.03251.71878.00640.75960.5452-0.312-0.7876-0.3009-0.07820.2651-0.0138-0.50640.69320.1849-0.02390.34350.0260.423215.9644-74.4891-60.4105
219.1985-4.84740.09496.1401-1.43266.42490.31280.48760.91850.9214-0.3317-0.051-0.2595-0.5511-0.12070.70720.0660.08090.453-0.0330.3859-6.0837-52.0187-28.8191
228.1138-3.4491-0.61925.24224.07153.8280.2116-0.51650.04471.0762-0.229-0.3990.2957-0.11150.28160.73410.01640.03110.59990.06160.3435-3.3193-60.8828-22.8429
232.76511.55983.17094.49534.95046.4328-0.5637-0.35220.4970.54960.52080.9635-0.5345-0.4023-0.03590.62230.10810.11550.67930.1020.4121-14.1085-57.0404-25.1868
249.35926.1297-6.29396.338-5.12934.3927-0.09310.17480.07950.19030.1356-0.10190.3056-0.2853-0.11210.46150.0415-0.03380.3923-0.00010.28280.6488-56.352-38.125
250.4251-1.4441-1.49796.12027.48329.73670.7228-0.81311.4522-0.5698-0.62760.3798-1.6865-1.8039-0.90850.85510.19370.11940.7398-0.09020.974514.544-46.7628-50.1278
263.66821.2624-3.2054.5595-2.32598.14340.3350.19960.27160.73620.48240.1853-0.29470.1693-0.46340.3735-0.0245-0.02060.28760.00960.441616.2679-53.962-49.4125
277.80065.023-0.96594.0683-1.50396.87180.0231-0.2218-0.24291.23730.2563-0.4339-0.171-0.0247-0.17440.47570.1507-0.01840.39940.03080.34887.2721-64.3-35.2696
283.92782.3416-3.04083.7447-3.52797.51220.02450.2393-0.058-0.1316-0.0391-0.08660.0398-0.2074-0.02670.29940.05230.00450.27820.00790.2915.8754-60.5324-53.1323
296.2639-4.49293.83536.556-4.91667.3643-0.2687-0.2170.20060.49280.0944-0.1837-0.7177-0.00970.05440.36610.03380.01550.2643-0.01980.346213.3345-67.322-48.5767
303.7705-2.60322.8898.45830.51753.301-0.072-0.27340.17330.60090.1531-0.61850.06570.4045-0.54140.37820.0760.03680.4630.08140.596223.1744-63.888-49.4483
310.5751-0.08811.51115.98690.4655.62250.0558-0.2354-0.24111.2219-0.299-0.1315-0.0184-0.48550.14340.4588-0.03150.08030.6630.11840.511212.1094-104.9232-16.2893
326.47-5.4613-0.62599.14493.6974.9584-0.8255-0.0453-0.05161.71840.19840.24450.0716-0.2530.48480.7620.05890.03550.60130.17320.544313.596-105.0652-14.4862
337.5292-3.9204-0.74583.8865-1.78265.00150.0630.7268-0.219-0.551-0.07150.47810.4567-0.1856-0.04120.5389-0.0699-0.07660.40520.03510.3856-16.1413-69.6791-16.2853
344.3647-2.7852-2.97967.59530.05728.5704-0.35650.4624-0.0806-0.11690.02570.11070.70.19410.3850.4911-0.0284-0.04360.54310.1070.3679-15.8289-68.2773-18.0085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 72 )
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 91 )
4X-RAY DIFFRACTION4chain 'A' and (resid 92 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 168 )
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 192 )
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 73 )
9X-RAY DIFFRACTION9chain 'B' and (resid 74 through 78 )
10X-RAY DIFFRACTION10chain 'B' and (resid 79 through 91 )
11X-RAY DIFFRACTION11chain 'B' and (resid 92 through 111 )
12X-RAY DIFFRACTION12chain 'B' and (resid 112 through 138 )
13X-RAY DIFFRACTION13chain 'B' and (resid 139 through 166 )
14X-RAY DIFFRACTION14chain 'B' and (resid 167 through 174 )
15X-RAY DIFFRACTION15chain 'B' and (resid 175 through 192 )
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 38 )
17X-RAY DIFFRACTION17chain 'C' and (resid 39 through 91 )
18X-RAY DIFFRACTION18chain 'C' and (resid 92 through 111 )
19X-RAY DIFFRACTION19chain 'C' and (resid 112 through 174 )
20X-RAY DIFFRACTION20chain 'C' and (resid 175 through 192 )
21X-RAY DIFFRACTION21chain 'D' and (resid 4 through 24 )
22X-RAY DIFFRACTION22chain 'D' and (resid 25 through 38 )
23X-RAY DIFFRACTION23chain 'D' and (resid 39 through 51 )
24X-RAY DIFFRACTION24chain 'D' and (resid 52 through 73 )
25X-RAY DIFFRACTION25chain 'D' and (resid 74 through 78 )
26X-RAY DIFFRACTION26chain 'D' and (resid 79 through 91 )
27X-RAY DIFFRACTION27chain 'D' and (resid 92 through 111 )
28X-RAY DIFFRACTION28chain 'D' and (resid 112 through 147 )
29X-RAY DIFFRACTION29chain 'D' and (resid 148 through 168 )
30X-RAY DIFFRACTION30chain 'D' and (resid 169 through 192 )
31X-RAY DIFFRACTION31chain 'E' and (resid 1 through 14 )
32X-RAY DIFFRACTION32chain 'F' and (resid 1 through 14 )
33X-RAY DIFFRACTION33chain 'G' and (resid 1 through 14 )
34X-RAY DIFFRACTION34chain 'H' and (resid 1 through 14 )

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  • 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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