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- PDB-2h71: Crystal Structure of Thioredoxin Mutant D47E in Hexagonal (p61) S... -

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Basic information

Entry
Database: PDB / ID: 2h71
TitleCrystal Structure of Thioredoxin Mutant D47E in Hexagonal (p61) Space Group
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / Alpha Beta
Function / homology
Function and homology information


DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin 1 / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsGavira, J.A. / Godoy-Ruiz, R. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
Citation
Journal: To be Published
Title: Crystal Structure of Thioredoxin Mutant D47E in Hexagonal (p61) Space Group
Authors: Godoy-Ruiz, R. / Gavira, J.A. / Ibarra-Molero, B. / Sanchez-Ruiz, J.M.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations.
Authors: Godoy-Ruiz, R. / Perez-Jimenez, R. / Ibarra-Molero, R. / Sanchez-Ruiz, R.
History
DepositionJun 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3May 2, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.6Apr 3, 2024Group: 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: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6394
Polymers23,4032
Non-polymers2362
Water1,72996
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9383
Polymers11,7011
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)11,7011
Polymers11,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.949, 102.949, 41.835
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Thioredoxin /


Mass: 11701.413 Da / Num. of mol.: 2 / Mutation: D47E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: trxA / Plasmid: pTk100 / Production host: Escherichia coli (E. coli) / Strain (production host): JF521 / References: UniProt: Q2M889, UniProt: P0AA25*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 53.33 %
Crystal growTemperature: 277 K / pH: 3.5
Details: 60% (v/v) MPD, Ac2Cu 1 mM, Hepes 15 mM pH 7.0, Counterdiffusion, temperature 277K, pH 3.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.07238
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07238 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 13367 / % possible obs: 98.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 49.98 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 28.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.044 / Mean I/σ(I) obs: 3.55 / % possible all: 97.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
HKL-2000data scaling
Cootmodel building
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRX_A

Resolution: 2.2→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 17.861 / SU ML: 0.23 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1281 9.895 %RANDOM
Rwork0.223 ---
obs0.23 12946 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.99 Å2
Baniso -1Baniso -2Baniso -3
1--5.017 Å2-2.508 Å20 Å2
2---5.017 Å20 Å2
3---7.525 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1626 0 16 96 1738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221743
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.9912379
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4265230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72326.47971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16315312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.47153
X-RAY DIFFRACTIONr_chiral_restr0.080.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021285
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2747
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21156
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4631.51127
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7521758
X-RAY DIFFRACTIONr_scbond_it1.3693702
X-RAY DIFFRACTIONr_scangle_it1.9264.5611
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 93 -
Rwork0.305 861 -
obs--99.79 %
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)
15.0732-3.45696.37412.3571-4.34668.0152-0.36830.35121.9155-0.9352-0.08360.7408-1.593-0.32810.45180.29270.0139-0.06230.26950.12370.2207-31.368387.412114.532
24.0819-1.15472.79316.80480.70442.2564-0.0274-0.06780.34460.50070.02880.56440.0888-0.46-0.00140.21510.00020.0320.17760.04620.1016-31.216384.40226.127
35.974-1.26770.62249.3820.9924.08680.0104-0.4950.00721.139-0.0510.92910.2055-0.21220.04070.3332-0.01690.11660.2590.06730.183-34.758878.724328.5175
44.6424-0.97022.90696.35661.62692.63250.0391-0.1477-0.28050.4968-0.01431.31530.3995-0.5188-0.02470.243-0.02250.06320.20590.0860.179-34.929473.083325.0888
57.13681.1737-1.18259.9218-1.91721.2560.2625-0.35550.22970.0584-0.29960.90960.0632-0.13430.0370.21010.0027-0.0430.19860.06490.1231-32.923672.4618.0442
62.57510.35440.74718.14591.23310.37520.0034-0.11120.26960.4414-0.0351-0.53660.0217-0.00630.03160.22380.0065-0.04290.20480.08080.1323-22.816781.88523.6675
72.68540.0509-0.83826.67730.37541.1636-0.0725-0.06250.66750.6014-0.009-1.4196-0.05790.04570.08160.2080.0123-0.1620.15750.06390.4456-15.440489.626825.9164
88.3998-1.4841.93047.6391-1.0532.66490.01190.12320.7421-0.1862-0.0537-1.472-0.1610.29740.04170.17650.00510.04850.1840.15190.3828-16.472488.727517.3721
96.65040.15991.69910.59090.30723.9841-0.00130.80810.5237-1.4478-0.1024-0.0343-0.1263-0.23160.10360.40870.02570.05490.32820.15580.18-23.9184.537711.1361
101.3210.9689-0.065311.7681-1.62783.97740.14120.73720.404-1.4478-0.12740.2599-0.28270.0016-0.01370.55760.0431-0.05490.38490.0910.1194-28.588177.78077.8768
112.96863.13413.39935.57052.18744.76210.04740.22640.0377-0.3455-0.04350.14680.24360.0437-0.00380.26470.015-0.02870.2520.09140.1149-28.967179.151516.3893
121.6822-0.12780.84466.90110.17732.9303-0.0663-0.52290.59011.2805-0.0234-0.477-0.0506-0.02740.08960.28430.0129-0.07570.17860.030.115-24.184386.735229.0961
132.9425-0.85911.57754.9523-1.83471.2479-0.0254-0.29640.05891.3123-0.0256-0.21850.2163-0.03890.05110.55530.0072-0.05130.29670.03320.0926-25.736681.760833.7268
142.78671.15782.842310.02141.28615.09620.0106-0.83060.21111.82410.0334-0.51330.05470.042-0.04390.5727-0.0031-0.10040.29920.0970.1121-23.563674.349633.0322
154.75711.3741-1.320710.0882-0.55860.37460.0002-0.5179-0.01561.26920.0158-1.35650.10210.1366-0.01590.32140.0246-0.1670.20470.06790.2804-16.966178.30528.1653
165.89751.56390.8066.7454-0.85460.29680.04510.3937-0.6475-0.2105-0.02740.10850.3726-0.1047-0.01770.25390.0005-0.02470.22570.07650.12-28.299670.170420.2985
172.311-2.75821.12167.21361.242.24630.02990.0299-0.45570.2405-0.0176-0.50810.2309-0.0486-0.01230.27830.0126-0.05220.22550.08460.1451-22.469369.887422.234
182.5955-0.28170.45318.3651-2.3880.73540.04520.15630.1441-0.1501-0.0373-1.61110.15730.0524-0.0080.13090.02120.05440.15420.10780.3907-13.032779.651617.8851
195.14781.1157-0.91626.00222.34291.28520.04540.7330.4829-1.255-0.0589-0.9938-0.3127-0.19080.01360.37760.03530.20860.30650.1340.2917-16.088979.523810.2211
204.0946-0.91881.135411.4915-1.17815.19640.09140.5059-0.4812-1.0873-0.073-0.68650.4525-0.0312-0.01840.330.04910.08460.25850.04780.1227-20.417671.17611.5248
212.09710.2108-1.09944.8877-2.96562.26070.1637-0.8971-0.83022.38840.0533-1.20210.20890.0403-0.2170.9962-0.0084-0.52070.35350.28530.7791-14.335351.462637.0056
223.5939-0.48520.01537.02210.27990.01150.2468-0.0961-0.6750.78880.0473-2.31130.14780.1855-0.29410.3780.059-0.37560.17660.07721.1668-5.776653.845626.2794
234.5651-0.9731.668.9442-2.63511.19980.2870.3526-1.02580.1249-0.0257-2.05430.27940.2088-0.26140.33060.0675-0.26610.14370.02621.1124-8.512447.999922.7662
242.2618-0.44381.828912.5333-0.95671.58360.34320.0927-1.18360.3343-0.0073-1.33410.3530.0873-0.3360.35290.0532-0.27070.12060.02861.0001-13.209543.464222.147
254.1575-1.96120.18145.7985-0.79160.96040.2446-0.093-1.11840.73580.0016-0.72420.3712-0.0071-0.24620.4092-0.0051-0.23160.14910.1440.5908-19.632448.745126.3428
262.00182.71740.864910.92023.2110.94930.1938-0.1205-0.51090.7767-0.0266-1.24530.1778-0.0266-0.16730.33660.0243-0.22040.17830.10390.492-14.5659.720526.1231
275.6309-0.8784-1.47.5810.84550.40110.0805-0.386-0.29121.17330.001-1.60110.16520.1853-0.08150.39130.0125-0.25210.21360.10160.3992-14.199968.952328.882
282.69090.71430.38454.56211.36660.46440.0792-0.3067-0.55551.41980.0449-0.71480.2534-0.0042-0.12420.7354-0.0161-0.20760.3350.18870.2934-20.993562.456834.3362
294.159-0.82362.22275.7299-0.34323.07090.1414-0.6814-0.64042.05860.0447-0.19320.0611-0.1516-0.18620.9917-0.0523-0.18640.38270.32230.4742-23.608852.926837.3639
304.5214-0.87980.27678.7109-0.54823.56770.2627-0.6075-1.43181.6053-0.0248-0.27330.5972-0.3295-0.23780.6893-0.0311-0.26260.23440.26230.6375-21.542947.446632.1899
314.82470.58760.93799.9028-0.31611.14450.18120.0835-0.41110.50520.0008-2.18840.09430.199-0.1820.2810.049-0.24740.16850.06710.8386-7.89561.135524.8009
323.055-0.4954-0.02126.3284-0.24990.01040.23510.4842-0.5986-0.5884-0.0401-1.69090.19470.0524-0.1950.26650.07550.04710.2041-0.02280.7158-10.277958.15515.6888
330.890.20530.20031.9035-0.37420.14030.25140.2913-0.8487-0.7027-0.0794-1.20580.47740.1737-0.1720.25320.06160.0530.1668-0.0090.3436-15.847460.736614.0098
343.3295-0.16770.52246.9202-1.30670.320.11160.2214-0.47430.0970.0034-0.76180.2787-0.186-0.1150.22710.016-0.08380.1590.07570.2463-18.197664.593822.2697
353.810.0327-0.22026.6353-1.70671.43260.22070.067-1.14180.2282-0.0189-0.45780.4356-0.0776-0.20190.28690.0104-0.15960.12590.06930.4708-21.148750.685321.9807
361.1967-3.34620.85419.4376-2.35770.6210.32270.4124-1.2023-0.586-0.0636-0.77610.520.1066-0.25920.33690.0394-0.17180.138-0.02470.725-19.258845.143617.9908
370.3875-1.6154-0.11466.74030.4780.03390.23450.2916-0.8584-0.3825-0.0518-0.13410.2144-0.0054-0.18260.23950.0097-0.09380.13330.03460.2792-24.638255.928218.6903
381.4654-0.2581-0.49944.82920.56070.240.1765-0.6027-0.68411.505-0.03560.28930.1957-0.1029-0.14090.5564-0.0405-0.02830.30070.18310.2497-27.601961.28630.9039
394.2347-1.9083-0.87316.56772.34862.27530.1832-0.4362-0.55131.1614-0.03970.6786-0.0226-0.313-0.14360.4635-0.0585-0.01040.23430.19370.3658-30.486456.236328.8279
405.5871-4.73062.604310.49071.8874.00460.26670.0172-1.44470.5609-0.11660.62220.6808-0.0071-0.15010.4113-0.0702-0.08270.17790.17940.6145-30.919648.325925.931
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 42 - 4
2X-RAY DIFFRACTION2AA5 - 95 - 9
3X-RAY DIFFRACTION3AA10 - 1510 - 15
4X-RAY DIFFRACTION4AA16 - 1916 - 19
5X-RAY DIFFRACTION5AA20 - 2320 - 23
6X-RAY DIFFRACTION6AA24 - 2824 - 28
7X-RAY DIFFRACTION7AA29 - 3529 - 35
8X-RAY DIFFRACTION8AA36 - 4036 - 40
9X-RAY DIFFRACTION9AA41 - 4741 - 47
10X-RAY DIFFRACTION10AA48 - 5248 - 52
11X-RAY DIFFRACTION11AA53 - 5653 - 56
12X-RAY DIFFRACTION12AA57 - 6257 - 62
13X-RAY DIFFRACTION13AA63 - 6763 - 67
14X-RAY DIFFRACTION14AA68 - 7168 - 71
15X-RAY DIFFRACTION15AA72 - 7972 - 79
16X-RAY DIFFRACTION16AA80 - 8380 - 83
17X-RAY DIFFRACTION17AA84 - 9084 - 90
18X-RAY DIFFRACTION18AA91 - 9591 - 95
19X-RAY DIFFRACTION19AA96 - 9996 - 99
20X-RAY DIFFRACTION20AA100 - 108100 - 108
21X-RAY DIFFRACTION21BB2 - 52 - 5
22X-RAY DIFFRACTION22BB6 - 106 - 10
23X-RAY DIFFRACTION23BB11 - 1511 - 15
24X-RAY DIFFRACTION24BB16 - 2016 - 20
25X-RAY DIFFRACTION25BB21 - 2421 - 24
26X-RAY DIFFRACTION26BB25 - 2825 - 28
27X-RAY DIFFRACTION27BB29 - 3629 - 36
28X-RAY DIFFRACTION28BB37 - 4237 - 42
29X-RAY DIFFRACTION29BB43 - 4943 - 49
30X-RAY DIFFRACTION30BB50 - 5650 - 56
31X-RAY DIFFRACTION31BB57 - 6457 - 64
32X-RAY DIFFRACTION32BB65 - 6965 - 69
33X-RAY DIFFRACTION33BB70 - 7370 - 73
34X-RAY DIFFRACTION34BB74 - 7774 - 77
35X-RAY DIFFRACTION35BB78 - 8278 - 82
36X-RAY DIFFRACTION36BB83 - 8683 - 86
37X-RAY DIFFRACTION37BB87 - 9187 - 91
38X-RAY DIFFRACTION38BB92 - 9692 - 96
39X-RAY DIFFRACTION39BB97 - 10397 - 103
40X-RAY DIFFRACTION40BB104 - 108104 - 108

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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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