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- PDB-3foz: Structure of E. coli Isopentenyl-tRNA transferase in complex with... -

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Basic information

Entry
Database: PDB / ID: 3foz
TitleStructure of E. coli Isopentenyl-tRNA transferase in complex with E. coli tRNA(Phe)
Components
  • (tRNA(Phe)) x 2
  • tRNA delta(2)-isopentenylpyrophosphate transferase
KeywordsTRANSFERASE/RNA / tRNA / nucleoside modification / isopentenyl-tRNA transferase / MiaA / TRANSFERASE-RNA COMPLEX
Function / homology
Function and homology information


regulation of cytoplasmic translation in response to stress / tRNA dimethylallyltransferase / tRNA dimethylallyltransferase activity / AMP dimethylallyltransferase activity / tRNA modification / cellular response to heat / ATP binding
Similarity search - Function
IPP transferase / Dimethylallyltransferase / IPP transferase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / tRNA dimethylallyltransferase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSeif, E. / Hallberg, B.M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: RNA-Protein Mutually Induced Fit: STRUCTURE OF ESCHERICHIA COLI ISOPENTENYL-tRNA TRANSFERASE IN COMPLEX WITH tRNA(Phe).
Authors: Seif, E. / Hallberg, B.M.
History
DepositionJan 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_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: tRNA delta(2)-isopentenylpyrophosphate transferase
B: tRNA delta(2)-isopentenylpyrophosphate transferase
C: tRNA(Phe)
D: tRNA(Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,20926
Polymers116,3284
Non-polymers88222
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-272 kcal/mol
Surface area46420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.240, 91.260, 152.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein tRNA delta(2)-isopentenylpyrophosphate transferase / MiaA / IPP transferase / Isopentenyl-diphosphate:tRNA isopentenyltransferase / IPTase / IPPT


Mass: 35107.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b4171, E. coli, JW4129, miaA, trpX / Plasmid: pNIC-BSA4 (GI: EF198106) / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: P16384, EC: 2.5.1.8
#2: RNA chain tRNA(Phe)


Mass: 23852.137 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TRNA WAS PREPARED BY IN-VITRO TRANSCRIPTION WITH T7
#3: RNA chain tRNA(Phe)


Mass: 22261.195 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TRNA WAS PREPARED BY IN-VITRO TRANSCRIPTION WITH T7
#4: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4K 15%, 0.2M CaCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2CaCl211
3PEG 400012
4CaCl212

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Double crystal monochromator, Si(111)
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→78.29 Å / Num. all: 43836 / Num. obs: 43749 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 51 Å2 / Rsym value: 0.097 / Net I/σ(I): 6.8
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2.14 / Rsym value: 0.493 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0044refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D3Q, 1TTT
Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.837 / SU B: 23.52 / SU ML: 0.239 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.576 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26822 2133 5 %RANDOM
Rwork0.24389 ---
all0.24517 43779 --
obs0.24517 40403 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.657 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å2-0 Å2
2--1.46 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4783 3055 22 73 7933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0218298
X-RAY DIFFRACTIONr_bond_other_d0.0010.024557
X-RAY DIFFRACTIONr_angle_refined_deg1.2792.42811945
X-RAY DIFFRACTIONr_angle_other_deg0.875311262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73123.158228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78815833
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2011548
X-RAY DIFFRACTIONr_chiral_restr0.0590.21451
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216928
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021319
X-RAY DIFFRACTIONr_mcbond_it4.41523036
X-RAY DIFFRACTIONr_mcbond_other1.36921216
X-RAY DIFFRACTIONr_mcangle_it6.15434866
X-RAY DIFFRACTIONr_scbond_it4.34425262
X-RAY DIFFRACTIONr_scangle_it5.70737079
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 139 -
Rwork0.382 2949 -
obs--97.35 %
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)
14.38160.46781.69791.63342.07215.4818-0.14840.19450.3292-0.1984-0.00290.2039-0.308-0.08870.15140.16840.01150.01640.03960.08660.2364.31734.95-22.108
20.3370.207-0.17961.12090.32211.93310.13230.0262-0.0087-0.0571-0.07820.25930.0808-0.2118-0.05420.10960.0201-0.02060.11090.00910.27080.75525.488-13.288
31.4328-1.22550.68652.042-1.01682.55290.05980.05710.0019-0.2217-0.0032-0.14390.0304-0.0572-0.05650.0525-0.0305-0.00540.09130.00510.246211.76319.329-15.917
42.23670.31530.67260.82060.55429.1326-0.0097-0.2242-0.15790.1241-0.042-0.11780.37750.33610.05160.07910.0087-0.01760.07690.03350.294229.8037.503-0.315
50.7816-0.448-0.07041.1861-0.46540.37660.00870.0686-0.0869-0.15580.03770.00080.02120.0237-0.04640.1482-0.00580.0160.1284-0.02650.267721.72215.5-15.415
68.4726-0.1887-8.60862.2772-1.920410.71950.24760.4160.22520.0022-0.0976-0.0704-0.3065-0.3465-0.150.2575-0.0046-0.06780.1108-0.01710.283213.56744.227-5.037
72.7433-2.61291.06263.606-0.36453.0742-0.0578-0.2979-0.09320.35230.0967-0.01260.0697-0.0901-0.03880.1088-0.01770.010.1320.00560.25875.62726.3516.342
81.51310.4688-0.18723.7849-1.72919.6061-0.1428-0.0088-0.02790.0684-0.0198-0.13190.1502-0.05010.16260.10560.02760.02110.1109-0.020.202411.87330.0558.856
91.4072-1.3796-3.42271.98742.144410.8167-0.0368-0.17270.12660.19770.1939-0.145-0.06820.3642-0.15720.1981-0.01350.01840.1039-0.030.232517.12137.3722.887
104.4632-1.33441.53991.40241.17155.1090.09660.16830.6088-0.3984-0.0643-0.2229-0.48190.0745-0.03230.2242-0.02720.03850.04520.06980.269913.04939.484-21.737
111.5997-0.3751-0.29032.0299-1.33967.6858-0.15540.0151-0.2394-0.19440.1197-0.24780.41980.44820.03570.18430.04160.00610.0667-0.02870.313822.78427.86241.373
122.27670.70821.09040.3310.66781.69350.0265-0.1264-0.39040.18870.0278-0.10150.61040.0289-0.05430.33660.0604-0.01080.11310.02880.27169.52424.38143.634
134.7002-0.30390.47381.8996-0.64244.37380.1450.1561-0.0280.2163-0.2718-0.26720.14790.39760.12680.17180.0296-0.01530.07890.02240.215517.5530.8647.54
144.4521-2.05961.18824.0308-0.50343.09460.30770.0330.15410.394-0.16220.4942-0.3585-0.4583-0.14560.24790.07630.14480.0983-0.01180.2459-7.28245.72852.103
152.13640.3314-1.19852.41990.58494.54680.167-0.11480.17770.3287-0.04480.0469-0.3087-0.1508-0.12220.27080.04590.06760.0312-0.03030.2655-1.5948.03955.156
161.0313-0.8672-0.49852.9249-4.204210.4994-0.0566-0.2942-0.05060.20210.2309-0.0506-0.28310.2284-0.17440.12730.0191-0.04980.1596-0.02210.315723.27935.51647.79
176.61927.09635.73919.43616.0275.1669-0.04770.3292-0.2786-0.07770.1841-0.5042-0.04510.3674-0.13650.13460.01540.02710.1252-0.01010.209115.53838.24324.163
185.8115-0.9577-4.93981.90671.22759.0302-0.04310.2161-0.0494-0.0649-0.12630.30880.3422-0.44830.16930.1728-0.0324-0.01060.0417-0.01050.2363-2.35625.54628.649
192.2320.79961.09590.43330.7291.66890.03250.14890.24410.0728-0.01090.1063-0.0381-0.09-0.02170.1923-0.00280.01020.04990.00360.29042.06137.55829.753
207.369-3.1185-0.66546.7818-0.34425.69920.1101-0.13880.1197-0.33340.0247-0.8721-0.0730.8928-0.13490.0591-0.017-0.03930.1408-0.02790.32429.33336.15438.341
214.0546-2.8087-3.87575.37330.38788.9117-0.15320.77070.57740.3024-0.4895-0.7998-0.2960.34840.64270.1576-0.1401-0.08590.61040.2390.539133.02555.71236.508
224.5534-1.87290.55141.97780.40740.4181-0.1034-0.4512-0.26470.10370.13050.0643-0.011-0.1398-0.0270.1790.05370.0620.2629-0.03580.262536.09347.93521.95
237.77740.53011.33663.791-0.31540.2838-0.00990.0782-0.19370.10210.07120.364-0.0325-0.0321-0.06120.11620.03250.0410.1831-0.03980.23434.67741.75611.797
247.6533-1.6102-0.88270.39990.77535.9088-0.05870.10030.29880.02390.009-0.05620.06210.14740.04960.1170.0314-0.00520.1502-0.00880.264453.48442.30516.081
250.921.02090.70531.29191.08961.31020.067-0.024-0.1502-0.01680.0585-0.2156-0.07180.1162-0.12560.1210.00670.01930.144-0.02880.295329.73931.929-3.263
261.58570.0001-0.23760.72620.47151.2409-0.0373-0.17450.04870.0471-0.0316-0.1240.0191-0.00230.06890.10660.01360.01870.07780.02130.286823.85325.494-5.215
275.67797.32443.74859.61045.70678.5523-0.9160.38550.4355-1.2480.32610.719-1.2036-0.49370.58990.38890.0419-0.10760.3535-0.12740.510639.42846.092.641
280.38690.1097-0.43330.6930.54122.11580.0136-0.06180.30930.03410.12240.0043-0.24150.2029-0.1360.18-0.0079-0.01290.0811-0.0680.380151.66652.86118.85
290.71510.8259-0.95911.1306-0.82811.8367-0.00210.11410.174-0.01730.2040.2004-0.1432-0.1521-0.2020.21150.03940.02170.2574-0.05890.409236.77255.53226.253
300.75611.62811.1493.5142.17412.96430.0583-0.1330.3540.1525-0.26940.7683-0.7819-0.87260.2110.15270.0067-0.01360.2147-0.03250.232424.38954.15140.51
310.49190.7943-1.91241.5974-3.89439.52380.05710.08090.1058-0.36680.09960.10030.9024-0.1794-0.15660.85410.0917-0.2060.2813-0.07820.5608-6.47660.2420.337
323.4099-1.07180.52729.3858-2.69521.35330.0820.1932-0.1548-0.1302-0.15540.19590.1842-0.12430.07330.2930.0607-0.0240.1305-0.02220.19020.12659.77214.494
331.11953.2074-0.20179.57670.6614.88640.0468-0.1292-0.0715-0.0203-0.4166-0.1827-0.05520.0990.36970.35850.12630.06560.15450.0760.15531.30378.2712.741
340.1266-0.39750.51971.6933-2.00542.4664-0.07760.06890.03580.39160.03730.0776-0.50960.06470.04020.35850.0274-0.05290.20220.06180.34415.05355.60926.156
350.52320.1335-0.62452.576-1.86432.18670.12140.01980.08490.2198-0.06660.3215-0.32380.0146-0.05480.21170.02330.00350.0537-0.01310.26553.89845.95841.977
367.07726.674.71176.2954.44833.14551.39580.7474-2.45861.47370.4744-2.39681.00250.4063-1.87031.33530.3724-0.3441.04710.66051.72889.77861.89318.131
371.75850.46280.5960.1290.16040.2113-0.06750.7595-0.2907-0.07090.1688-0.1104-0.10410.243-0.10130.79980.19520.16090.46210.02170.23226.00172.904-0.185
382.13570.97480.20329.27940.11422.00640.03470.3702-0.0483-0.2797-0.015-0.188-0.16990.0551-0.01980.27840.05320.01580.17990.02470.16883.26877.5246.429
390.0691-0.293809.1213011.25010.22970.15670.0463-1.2817-0.5565-0.28931.20340.46090.32670.92140.38930.1440.5471-0.03290.2810.86867.46-6.307
403.23480.98953.28920.36980.62986.92830.4452-0.6092-1.10090.0503-0.3409-0.33570.78380.0737-0.10440.6571-0.0283-0.26280.55250.0831.0815-8.42752.69-5.033
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 33
2X-RAY DIFFRACTION2A34 - 99
3X-RAY DIFFRACTION3A100 - 131
4X-RAY DIFFRACTION4A132 - 153
5X-RAY DIFFRACTION5A154 - 204
6X-RAY DIFFRACTION6A205 - 221
7X-RAY DIFFRACTION7A222 - 247
8X-RAY DIFFRACTION8A248 - 263
9X-RAY DIFFRACTION9A264 - 280
10X-RAY DIFFRACTION10A281 - 311
11X-RAY DIFFRACTION11B10 - 42
12X-RAY DIFFRACTION12B43 - 96
13X-RAY DIFFRACTION13B97 - 114
14X-RAY DIFFRACTION14B115 - 153
15X-RAY DIFFRACTION15B154 - 191
16X-RAY DIFFRACTION16B192 - 204
17X-RAY DIFFRACTION17B205 - 219
18X-RAY DIFFRACTION18B220 - 241
19X-RAY DIFFRACTION19B242 - 287
20X-RAY DIFFRACTION20B288 - 311
21X-RAY DIFFRACTION21C1 - 4
22X-RAY DIFFRACTION22C5 - 8
23X-RAY DIFFRACTION23C9 - 15
24X-RAY DIFFRACTION24C16 - 20
25X-RAY DIFFRACTION25C21 - 34
26X-RAY DIFFRACTION26C35 - 43
27X-RAY DIFFRACTION27C44 - 47
28X-RAY DIFFRACTION28C48 - 61
29X-RAY DIFFRACTION29C62 - 70
30X-RAY DIFFRACTION30C71 - 74
31X-RAY DIFFRACTION31D4 - 7
32X-RAY DIFFRACTION32D8 - 16
33X-RAY DIFFRACTION33D17 - 20
34X-RAY DIFFRACTION34D21 - 30
35X-RAY DIFFRACTION35D31 - 43
36X-RAY DIFFRACTION36D44 - 47
37X-RAY DIFFRACTION37D48 - 55
38X-RAY DIFFRACTION38D56 - 61
39X-RAY DIFFRACTION39D62 - 66
40X-RAY DIFFRACTION40D67 - 72

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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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