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- PDB-3wu4: Oxidized-form structure of E.coli Lon Proteolytic domain -

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Basic information

Entry
Database: PDB / ID: 3wu4
TitleOxidized-form structure of E.coli Lon Proteolytic domain
ComponentsLon proteaseLon protease family
KeywordsHYDROLASE / OXIDIZED FORM / LON PROTEASE / CATALYTIC DYAD SER-LYS / ATP BINDING
Function / homologyRibosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNishii, W. / Kukimoto-Niino, M. / Terada, T. / Shirouzu, M. / Muramatsu, T. / Yokoyama, S.
CitationJournal: Nat. Chem. Biol. / Year: 2015
Title: A redox switch shapes the Lon protease exit pore to facultatively regulate proteolysis.
Authors: Nishii, W. / Kukimoto-Niino, M. / Terada, T. / Shirouzu, M. / Muramatsu, T. / Kojima, M. / Kihara, H. / Yokoyama, S.
History
DepositionApr 22, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lon protease
B: Lon protease
C: Lon protease
D: Lon protease
E: Lon protease
F: Lon protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,67911
Polymers128,1996
Non-polymers4805
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lon protease


Theoretical massNumber of molelcules
Total (without water)21,3671
Polymers21,3671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Lon protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4632
Polymers21,3671
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Lon protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4632
Polymers21,3671
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Lon protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4632
Polymers21,3671
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
E: Lon protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4632
Polymers21,3671
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: Lon protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4632
Polymers21,3671
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.391, 86.391, 124.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Lon protease / Lon protease family


Mass: 21366.500 Da / Num. of mol.: 6
Fragment: C-TERMINAL PROTEOLYTIC DOMAIN, UNP RESIDUES 585-784
Mutation: S679A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12, W3110 / Gene: lon, EcDH1_3170, ECDH1ME8569_0424 / Plasmid: PMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9QQ79, endopeptidase La
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.1M AMMONIUM SULFATE, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 111242 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.06 / Net I/σ(I): 24.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.88 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RR9
Resolution: 1.7→37.41 Å / σ(F): 1.97 / Phase error: 32.08 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.177 5596 5.03 %
Rwork0.152 --
obs0.156 111228 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→37.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8158 0 25 314 8497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078301
X-RAY DIFFRACTIONf_angle_d0.98111273
X-RAY DIFFRACTIONf_dihedral_angle_d13.8933102
X-RAY DIFFRACTIONf_chiral_restr0.0621365
X-RAY DIFFRACTIONf_plane_restr0.0051462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7003-1.72960.34742830.3551530493
1.7296-1.7610.31372810.3121534094
1.761-1.79480.33942870.291528594
1.7948-1.83140.30652630.2743536694
1.8314-1.87120.24913290.2387533393
1.8712-1.91460.22862630.2182537594
1.9146-1.96240.23792740.2149541594
1.9624-2.01540.20352970.1966531894
2.0154-2.07460.20322600.1893540395
2.0746-2.14140.18062900.1733533494
2.1414-2.21780.18642480.1766547495
2.2178-2.30630.17912990.1597533394
2.3063-2.4110.18872800.162542595
2.411-2.53770.20172840.1716542395
2.5377-2.6960.18652810.1591539395
2.696-2.90310.15692920.1487540095
2.9031-3.19330.16742560.1371545995
3.1933-3.65080.14673260.1174530693
3.6508-4.58270.15052800.1008494686
4.5827-16.32710.14531930.1288400470
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)
12.45070.16072.21313.34841.21513.68660.15930.0332-0.0785-0.0292-0.1990.00910.13740.29190.0960.1746-0.0020.01990.27940.00580.1722-68.0798101.6992-37.1173
21.7449-0.6858-0.87952.05690.06881.0744-0.1018-0.18830.0970.15740.0202-0.0755-0.08260.16090.08790.1887-0.0101-0.03160.245-0.00570.1542-67.1338112.9225-30.6215
32.255-0.1-0.10121.5665-0.23220.80560.0341-0.4214-0.0110.3978-0.06970.076-0.0712-0.0288-0.01420.2594-0.02330.02050.3174-0.0150.1092-70.3378107.3379-26.9504
43.2351-0.55282.22781.4555-0.32744.09040.069-0.1459-0.20170.0168-0.08340.10630.1878-0.2263-0.08770.1922-0.03640.01570.2618-0.01510.1483-79.5064105.2342-35.0435
54.634-1.0324-0.31775.87291.13364.18270.08590.4841-0.3458-0.524-0.23140.28180.0599-0.18670.03850.2274-0.0236-0.01770.2801-0.08180.184-82.08599.9024-46.3397
62.37490.27021.29433.39721.20335.4320.1013-0.216-0.17590.1317-0.12660.07010.2221-0.22970.06370.1758-0.05980.0220.2761-0.00790.1889-84.924998.6994-37.6554
72.9478-0.33091.33652.1252-0.03053.8159-0.02850.1804-0.2018-0.03120.1345-0.4049-0.25560.4022-0.06210.2268-0.02860.03860.2460.02250.3731-40.9217100.2559-33.4485
82.27771.0897-0.47961.7683-0.19412.52010.0637-0.23970.1410.20410.0173-0.0836-0.1691-0.182-0.11270.18920.0294-0.01960.2305-0.00490.1966-50.8354106.9659-28.7662
92.97850.9723-0.36322.7120.29092.05430.0511-0.3771-0.11450.3112-0.0665-0.0790.0054-0.02210.03440.17060.0095-0.01470.23980.04560.174-47.914101.8963-24.4255
101.25610.3123-0.25162.4481.07934.13930.0419-0.0852-0.34920.0697-0.0038-0.11350.11190.1089-0.09810.1979-0.0035-0.00860.21030.06880.2473-49.990492.1915-32.034
114.7143-0.16290.30995.1989-0.50034.34070.09090.3286-0.5702-0.61-0.2493-0.56090.27370.4070.14250.28480.03460.06040.2190.01560.4299-45.38285.0015-41.5967
127.7994-0.39941.32376.7776-1.72621.7377-0.0254-0.7799-0.60150.4253-0.0247-0.473-0.1058-0.1670.13830.29170.007-0.01610.32260.12910.3174-48.539187.259-23.8308
132.5646-0.3804-0.1463.63920.71462.09420.04730.00540.19830.0498-0.00960.0613-0.03130.0044-0.10880.1647-0.00130.00480.2119-0.01050.1977-32.4388120.5862-28.7791
142.5662-0.47750.50934.8146-1.50313.5764-0.0559-0.489-0.20580.67340.02440.13120.1241-0.17440.04710.28940.00270.0210.31890.00430.2351-34.2851117.6486-16.309
151.1897-0.7001-0.39292.3411-0.13142.1802-0.0212-0.1454-0.0250.0935-0.0501-0.0237-0.04050.13080.01550.1839-0.0050.00020.23220.02180.2207-28.9345119.741-28.597
161.8011-0.6685-0.7652.01210.84393.4616-0.1017-0.1284-0.1710.20520.1218-0.12210.12930.2821-0.03460.17480.0268-0.0210.25090.03450.1563-24.1028111.6197-28.4755
173.66141.9039-0.69946.87971.10353.3392-0.01130.1835-0.199-0.12360.2144-0.1955-0.0280.1316-0.20020.16290.0202-0.01480.3238-0.01250.2257-16.0998112.0108-38.625
183.3316-0.3901-2.322.39981.64413.2525-0.0629-0.3192-0.02750.32210.177-0.07620.26640.2808-0.10080.18780.0275-0.04010.31820.02960.2497-15.395110.4503-28.6121
191.81920.36610.57882.83090.58480.2673-0.08620.37470.7433-0.13780.21690.2022-0.1586-0.39290.17430.2101-0.0325-0.07870.34880.0240.3977-39.076147.772-30.5477
201.7778-0.57281.13532.0507-1.19854.3458-0.1123-0.29460.09610.11160.01130.02530.205-0.22410.0750.1955-0.0020.01230.232-0.03880.2428-40.4837135.4385-25.7841
213.87560.78470.02962.3557-0.65923.7763-0.0992-0.5513-0.30860.4363-0.1264-0.2278-0.0051-0.01480.20780.2820.028-0.01350.303-0.0250.3697-41.1264138.2008-16.1136
222.32460.5570.00080.7702-0.26482.7903-0.0645-0.12490.1840.0826-0.0403-0.01780.0051-0.00050.26580.22270.0096-0.03640.2289-0.010.3254-37.7916143.445-28.2872
233.32131.5251-1.68793.5057-1.04213.8939-0.00850.010.56760.0090.1229-0.034-0.19240.0326-0.0770.1457-0.0304-0.04490.2069-0.02350.3164-28.245147.3938-31.1217
246.6935-0.2389-0.03728.29220.60466.64240.05240.06480.1351-0.71160.2352-0.86890.03460.6581-0.18340.262-0.07290.060.2779-0.00110.466-19.0144145.8394-35.6734
253.83922.2416-1.8535.014-1.90954.1736-0.0407-0.2390.39780.1084-0.1777-0.2755-0.11220.25050.20360.1855-0.032-0.07650.2808-0.0120.4285-22.8903150.0767-26.7104
262.2079-0.0339-2.2350.8907-0.67222.87820.05660.11360.3809-0.17630.12070.2260.1979-0.24930.01640.2222-0.0262-0.03360.2253-0.02050.3896-67.9544149.3605-32.3506
272.8834-0.1931-0.6111.37271.7096.066-0.0061-0.2515-0.00410.14760.1420.07030.1693-0.06780.07850.2146-0.0148-0.02090.1994-0.02940.2398-62.1362137.2397-27.9088
282.5309-0.1045-0.85182.45320.86334.0089-0.1013-0.43630.38710.26330.0811-0.0270.06530.386-0.08340.17390.0161-0.03940.2686-0.07340.2659-54.5297146.1889-24.4478
291.92460.78670.28482.86442.03932.49420.0332-0.51160.21930.66120.0004-0.21560.1835-0.1457-0.04150.30460.0148-0.06780.2952-0.09730.3039-63.2848141.5091-18.6092
301.33740.1618-0.10483.32112.0543.5286-0.0847-0.16490.3183-0.0093-0.02620.04210.1174-0.13620.09260.16780.0052-0.03190.2062-0.03130.2788-62.4692147.9529-31.0593
312.18990.1245-1.48992.5373-0.80214.5280.11620.0010.85850.04280.1512-0.0597-0.0365-0.0171-0.13990.1951-0.0139-0.02730.2237-0.05330.4694-57.8438156.2215-29.7893
329.6432-1.1832-3.17174.9165-1.11034.98160.12530.51830.2091-0.2065-0.0239-0.0402-0.2969-0.184-0.15410.28130.04960.10660.35510.09670.6981-65.6196160.7562-42.3636
332.00641.5036-1.94084.0527-1.10793.95640.39080.36790.6876-0.07550.18670.5168-0.4714-0.1535-0.42960.34250.00610.05450.3160.05560.9023-57.7053166.4333-37.9142
340.49941.49491.32725.67674.55343.7781-0.0285-0.0097-0.36130.21260.01660.34890.12670.0721-0.0170.2870.01660.02110.2608-0.03990.4465-60.5842163.5215-16.1708
352.9619-0.07610.82962.5062-0.97443.1584-0.1468-0.06260.1046-0.12230.04760.1440.2871-0.2070.00360.2353-0.0136-0.01410.2198-0.03980.2436-80.1483125.1978-37.1584
361.85950.6358-0.18922.21411.46872.93930.0486-0.18820.16870.1611-0.0168-0.08660.05680.09480.05410.1979-0.0105-0.03990.2214-0.02440.1784-70.3285129.9373-30.336
378.793-3.06891.07546.9237-0.97395.7012-0.1004-0.55870.52860.8653-0.11420.04850.1465-0.08250.11210.3621-0.05410.02050.3619-0.0530.2663-76.4645133.4296-15.9844
381.9507-0.39950.76483.2869-0.41080.9431-0.0787-0.16510.16490.10420.06260.05510.0698-0.077-0.02920.18850.0089-0.02560.2311-0.01510.1184-74.6375124.5902-35.5622
392.6840.35980.05633.138-0.94034.0083-0.0241-0.27740.41750.160.07010.27620.0551-0.2244-0.10390.14680.01690.00020.2301-0.05950.2045-82.8629134.5419-31.6809
404.01951.00440.55056.67480.33854.7414-0.10280.15320.4208-0.35490.15080.2699-0.0807-0.18490.04330.19880.0042-0.09450.26660.05340.3346-89.0483137.2502-45.6314
413.66750.08861.84863.0604-0.38436.767-0.06-0.24960.31410.05310.07860.4793-0.0575-0.5955-0.08090.15910.0336-0.01180.2848-0.01920.3519-92.0113137.6063-36.8843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 596:619 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 620:647 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 648:693 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 694:718 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 719:746 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 747:773 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 595:619 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 620:647 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 648:693 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 694:718 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 719:762 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 763:774 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 595:647 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 648:669 )
15X-RAY DIFFRACTION15CHAIN C AND (RESID 670:693 )
16X-RAY DIFFRACTION16CHAIN C AND (RESID 694:718 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 719:746 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 747:775 )
19X-RAY DIFFRACTION19CHAIN D AND (RESID 594:619 )
20X-RAY DIFFRACTION20CHAIN D AND (RESID 620:648 )
21X-RAY DIFFRACTION21CHAIN D AND (RESID 649:669 )
22X-RAY DIFFRACTION22CHAIN D AND (RESID 670:693 )
23X-RAY DIFFRACTION23CHAIN D AND (RESID 694:732 )
24X-RAY DIFFRACTION24CHAIN D AND (RESID 733:746 )
25X-RAY DIFFRACTION25CHAIN D AND (RESID 747:775 )
26X-RAY DIFFRACTION26CHAIN E AND (RESID 591:619 )
27X-RAY DIFFRACTION27CHAIN E AND (RESID 620:631 )
28X-RAY DIFFRACTION28CHAIN E AND (RESID 632:652 )
29X-RAY DIFFRACTION29CHAIN E AND (RESID 653:669 )
30X-RAY DIFFRACTION30CHAIN E AND (RESID 670:693 )
31X-RAY DIFFRACTION31CHAIN E AND (RESID 694:718 )
32X-RAY DIFFRACTION32CHAIN E AND (RESID 719:732 )
33X-RAY DIFFRACTION33CHAIN E AND (RESID 733:762 )
34X-RAY DIFFRACTION34CHAIN E AND (RESID 763:784 )
35X-RAY DIFFRACTION35CHAIN F AND (RESID 595:619 )
36X-RAY DIFFRACTION36CHAIN F AND (RESID 620:647 )
37X-RAY DIFFRACTION37CHAIN F AND (RESID 648:661 )
38X-RAY DIFFRACTION38CHAIN F AND (RESID 662:680 )
39X-RAY DIFFRACTION39CHAIN F AND (RESID 681:718 )
40X-RAY DIFFRACTION40CHAIN F AND (RESID 719:746 )
41X-RAY DIFFRACTION41CHAIN F AND (RESID 747:773 )

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