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- PDB-5d5o: HcgC from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 5d5o
TitleHcgC from Methanocaldococcus jannaschii
ComponentsUncharacterized protein MJ0489
KeywordsUNKNOWN FUNCTION / Rossmann-like fold
Function / homologyFeGP cofactor biosynthesis protein, methyltransferase HcgC / FeGP cofactor biosynthesis protein, methyltransferase HcgC / Uncharacterized protein MJ0489
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
Funding support Japan, Germany, 2items
OrganizationGrant numberCountry
JST-PRESTO Japan
Max Planck Society Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Identification of HcgC as a SAM-Dependent Pyridinol Methyltransferase in [Fe]-Hydrogenase Cofactor Biosynthesis.
Authors: Fujishiro, T. / Bai, L. / Xu, T. / Xie, X. / Schick, M. / Kahnt, J. / Rother, M. / Hu, X. / Ermler, U. / Shima, S.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein MJ0489
B: Uncharacterized protein MJ0489
C: Uncharacterized protein MJ0489
D: Uncharacterized protein MJ0489
E: Uncharacterized protein MJ0489
F: Uncharacterized protein MJ0489
G: Uncharacterized protein MJ0489
H: Uncharacterized protein MJ0489
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,6259
Polymers244,5298
Non-polymers961
Water68538
1
A: Uncharacterized protein MJ0489
B: Uncharacterized protein MJ0489
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2283
Polymers61,1322
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-32 kcal/mol
Surface area21370 Å2
MethodPISA
2
C: Uncharacterized protein MJ0489
D: Uncharacterized protein MJ0489


Theoretical massNumber of molelcules
Total (without water)61,1322
Polymers61,1322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-18 kcal/mol
Surface area21910 Å2
MethodPISA
3
E: Uncharacterized protein MJ0489
F: Uncharacterized protein MJ0489


Theoretical massNumber of molelcules
Total (without water)61,1322
Polymers61,1322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-18 kcal/mol
Surface area21680 Å2
MethodPISA
4
G: Uncharacterized protein MJ0489
H: Uncharacterized protein MJ0489


Theoretical massNumber of molelcules
Total (without water)61,1322
Polymers61,1322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-16 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.250, 143.280, 148.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B
31chain C and segid C
41chain D and segid D
51chain E and segid E
61chain F and segid F
71chain G and segid G
81chain H and segid H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0
311chain C and segid CC0
411chain D and segid DD0
511chain E and segid EE0
611chain F and segid FF0
711chain G and segid GG0
811chain H and segid HH0

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Components

#1: Protein
Uncharacterized protein MJ0489 / HcgC


Mass: 30566.113 Da / Num. of mol.: 8 / Fragment: Rossmann-like domain, residues 1-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0489 / Plasmid: pET24b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57913
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 27 % (v/v) PEG400, 45 mM Tris-HCl, 45 mM sodium sulfate, 45 mM lithium sulfate and 0.2 M 2,2,2-trifuloroethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2012
RadiationMonochromator: A double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 149108 / % possible obs: 92.7 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 52.85 Å2 / Rmerge F obs: 0.33 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.156 / Χ2: 1.107 / Net I/σ(I): 7.72 / Num. measured all: 405877
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.7-2.81.4620.8181.594362216599158781.00895.7
2.8-31.0430.582.357055126949257790.71895.7
3-3.40.6160.3224.099094236722346490.40494.4
3.4-4.10.2540.1368.798722534670318090.1791.7
4.1-5.90.1220.07113.887529830517276200.08890.5
5.9-80.0980.05616.4523404924481170.06987.8
8-120.0440.03523.1210046436537210.04385.2
120.0370.03626.344789184715350.04383.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.326 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2628 4163 5.26 %
Rwork0.2166 74978 -
obs0.2191 79141 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.09 Å2 / Biso mean: 61.3534 Å2 / Biso min: 24.37 Å2
Refinement stepCycle: final / Resolution: 2.7→48.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15862 0 5 38 15905
Biso mean--164.27 39.49 -
Num. residues----1966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816155
X-RAY DIFFRACTIONf_angle_d1.25421867
X-RAY DIFFRACTIONf_chiral_restr0.0532558
X-RAY DIFFRACTIONf_plane_restr0.0062757
X-RAY DIFFRACTIONf_dihedral_angle_d13.2355987
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9511X-RAY DIFFRACTION12.24TORSIONAL
12B9511X-RAY DIFFRACTION12.24TORSIONAL
13C9511X-RAY DIFFRACTION12.24TORSIONAL
14D9511X-RAY DIFFRACTION12.24TORSIONAL
15E9511X-RAY DIFFRACTION12.24TORSIONAL
16F9511X-RAY DIFFRACTION12.24TORSIONAL
17G9511X-RAY DIFFRACTION12.24TORSIONAL
18H9511X-RAY DIFFRACTION12.24TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.73070.39881390.33872522266198
2.7307-2.76280.38151140.31232580269497
2.7628-2.79650.35491300.30952563269398
2.7965-2.83190.39421090.31032537264697
2.8319-2.86910.33181090.32593270297
2.8691-2.90840.3631620.29292530269297
2.9084-2.950.34041550.27592482263797
2.95-2.9940.32141700.2832503267396
2.994-3.04080.37481470.28492542268997
3.0408-3.09060.30441400.28512555269597
3.0906-3.14390.33361320.28282492262496
3.1439-3.20110.29981300.26972548267896
3.2011-3.26260.31041500.25442524267496
3.2626-3.32920.30841380.24772503264196
3.3292-3.40160.3061710.22852476264796
3.4016-3.48070.26221180.23742552267095
3.4807-3.56770.24251180.21142516263496
3.5677-3.66410.28161110.2112536264795
3.6641-3.77190.24771250.21832481260694
3.7719-3.89360.25511420.22412502264494
3.8936-4.03270.22521420.20812493263594
4.0327-4.19410.2361620.18362459262194
4.1941-4.38480.23191180.16742503262194
4.3848-4.61590.23671260.15582457258393
4.6159-4.90480.21141410.16152485262693
4.9048-5.28310.20951380.16972455259392
5.2831-5.81390.23441790.19152415259492
5.8139-6.65340.2371930.19692378257190
6.6534-8.37540.22291140.18792435254988
8.3754-48.33370.22281400.19332361250183
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)
12.0739-0.7145-0.24889.88267.36846.4258-0.19990.5250.3004-1.039-0.15230.5247-0.9362-0.02290.42010.44230.0495-0.1040.54170.13330.3492-28.461440.3046-21.9332
22.39551.97435.35115.40152.68978.6251-0.11590.40070.5748-0.4358-0.04640.5119-0.1975-0.23560.04850.43830.0161-0.09840.72820.00180.5212-34.898524.9264-31.0771
37.59433.5640.4118.9542-0.10398.1203-0.08220.04910.44120.0859-0.32561.1523-0.0102-1.29010.25930.33280.0494-0.01680.7675-0.08530.3632-41.507116.3347-27.4979
42.62031.89482.53523.03644.11544.28640.08860.0988-0.3320.06670.0011-0.17610.2636-0.0917-0.09210.30640.02810.01260.4958-0.00890.3069-23.282617.5846-20.9576
50.87311.03680.04895.4553.38563.2154-0.07820.11770.2541-0.2077-0.05110.6834-0.019-0.16070.14660.33230.097-0.10490.39520.06250.4118-27.813641.3798-13.1066
63.17463.74631.64183.10255.68938.48450.5476-0.83980.54021.8077-1.13170.97381.2721-0.21690.62830.4949-0.02220.10440.7088-0.07210.4638-27.530641.383612.12
76.2425-0.60250.68543.2896-1.01682.08660.0701-1.0370.56020.8056-0.51891.43390.0046-1.47590.39290.6186-0.10150.25381.3299-0.54671.171-33.957958.643820.7103
83.1667-1.057-2.44724.72112.57397.78220.1048-0.86161.3203-0.50350.29041.2091-1.62-0.401-0.1920.7275-0.02740.15121.0661-0.49581.1555-31.07469.644916.7408
93.2965-1.8805-4.07484.8014.65559.81360.6245-1.0641.26180.46470.5472-0.5004-1.27020.6986-0.99120.6795-0.09220.09990.61-0.20470.7658-16.914365.65848.8426
101.37421.6198-0.13535.20232.38182.525-0.0853-0.08970.56580.11090.02060.4988-0.1035-0.10060.02910.22220.03140.03230.3717-0.01240.4586-23.667444.52492.6589
112.25090.84920.15083.64562.75664.25350.0216-0.21730.40780.1446-0.17490.3579-0.1249-0.09420.14680.3261-0.06020.07610.57190.060.3532-27.864140.19776.2035
120.89411.61831.50716.99865.78854.5815-0.24330.14820.3516-1.5340.3514-0.0865-1.43880.3579-0.05180.7148-0.13970.0440.44760.09830.49787.72361.0334-5.5382
138.62862.26893.38225.64041.28437.4312-0.29650.54980.4236-0.56380.2-1.0241-0.56120.92330.1750.4984-0.08870.05010.4286-0.03560.597717.956865.64826.6385
146.08715.35313.24899.86182.87223.1964-0.0981-0.59310.49070.1671-0.25920.5731-0.22690.14990.30850.34910.06240.06850.4207-0.02810.30332.815963.111811.9282
150.57161.61080.92924.41484.09553.5122-0.11140.1768-0.034-0.38650.0844-0.0463-0.5560.2899-0.00590.4129-0.05110.05610.35710.12950.32535.355847.197-8.888
16-0.2292-0.6073-1.36937.46464.45354.0869-0.3065-0.3436-0.25820.67280.5664-0.25840.71450.6363-0.27020.31970.1383-0.05050.46450.0950.42497.159316.6209-7.9308
175.6096-1.211-2.25027.65312.14557.02350.2118-0.41360.194-0.1506-0.1657-0.76410.15721.1706-0.04040.30320.10.05670.48160.07780.319415.097910.3176-24.1589
183.5517-3.4932-1.93188.35262.30242.87160.09980.5444-0.4729-0.8212-0.36221.0708-0.06790.10050.23460.33740.08-0.14590.4137-0.03160.4371-1.732316.5524-26.6984
190.48260.0570.4875.28613.40732.9896-0.00740.11870.01620.1406-0.0685-0.02460.09720.26450.07630.24430.06510.00480.41170.14050.3313.236630.2832-5.0643
202.05332.964-3.33135.9171-6.68389.1953-0.1673-0.68780.39561.3008-0.1401-0.4343-0.91970.1947-0.01940.43390.22560.08750.76940.00250.352923.837440.243-52.3036
218.2192-1.00910.42858.38681.01446.7135-0.0841-0.07050.30580.2632-0.0602-0.71410.12450.75920.26650.38490.16680.06280.73460.10850.427333.981919.9779-45.317
221.7332-0.94430.84642.977-2.0754.2156-0.02080.1333-0.2098-0.30760.0157-0.10590.332-0.03750.00970.39830.11630.11960.51530.00690.350218.385317.4849-53.2128
231.43460.9837-0.15756.2655-3.48523.3373-0.0091-0.07-0.0691-0.1392-0.0773-0.52330.05610.57560.0370.32850.06180.04990.5608-0.12790.337523.064941.3009-61.1004
241.6112-0.0766-0.58412.3524-3.06123.8210.29010.93040.0494-1.3229-0.6875-0.75390.86240.22520.31270.85960.22820.21470.79070.02520.570222.601241.3745-86.335
253.26990.4007-2.18721.7757-1.18097.1540.53210.86461.0006-0.614-0.5673-0.963-0.53971.0301-0.00090.72160.16440.3211.00570.37440.962223.817864.576-90.4583
261.7658-0.79280.15342.8706-0.96471.13540.00840.21890.2589-0.207-0.0471-0.40930.07540.18540.01930.47080.15850.14650.64450.0420.38122.547645.093-76.6077
270.9971-0.71270.18562.7134-2.29421.55960.30650.20250.1038-0.9165-0.2857-0.16570.43750.2455-0.15370.64040.14420.05160.6728-0.04880.302317.371537.3712-82.1144
281.16182.0335-2.13448.3995-6.42195.295-0.283-0.96420.76610.91720.46140.0455-0.8165-0.8166-0.08310.38540.0067-0.06830.0628-0.20760.6891-10.785356.031-63.504
297.4483-0.45823.13516.7668-0.7786.16850.112-0.52-0.0609-0.26550.00161.07280.006-0.9509-0.13960.27520.0073-0.01850.56430.00030.6522-21.194967.6794-79.8467
305.4634-4.02731.64417.1959-3.10183.91030.13070.48160.3884-0.5695-0.25420.119-0.22450.13490.14630.3996-0.0647-0.07120.3044-0.01640.4534-7.712363.3392-85.6422
310.4657-0.5432-0.08276.3829-2.85853.00840.06960.058-0.0231-0.3579-0.08610.27750.28940.02370.07520.29010.03930.03440.35-0.13230.3152-10.155547.2834-65.0837
320.3791.2247-0.76853.7186-5.84158.095-0.23380.1102-0.2131-0.97190.37260.00950.9448-0.3731-0.14810.74070.02880.03180.395-0.10920.5056-13.765115.7794-64.0522
332.30393.1002-1.30514.3892-2.19211.9707-0.0315-0.2084-0.3511-0.3595-0.291-0.6670.57980.27360.34160.53920.16260.05840.308-0.00770.4919-6.885715.7644-49.8022
340.8886-0.20950.11924.4202-2.23964.47790.0120.1064-0.2245-0.46570.00520.18420.4194-0.0171-0.00590.4128-0.0727-0.03790.291-0.07810.3365-9.891332.0195-70.7513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 42 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 69 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 116 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 184 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 268 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 42 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 96 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 97 through 139 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 140 through 166 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 167 through 221 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 222 through 268 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 13 through 55 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 56 through 105 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 106 through 184 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 185 through 268 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 13 through 69 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 70 through 116 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 117 through 166 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 167 through 268 )D0
20X-RAY DIFFRACTION20chain 'E' and (resid 13 through 42 )E0
21X-RAY DIFFRACTION21chain 'E' and (resid 43 through 116 )E0
22X-RAY DIFFRACTION22chain 'E' and (resid 117 through 184 )E0
23X-RAY DIFFRACTION23chain 'E' and (resid 185 through 268 )E0
24X-RAY DIFFRACTION24chain 'F' and (resid 13 through 42 )F0
25X-RAY DIFFRACTION25chain 'F' and (resid 43 through 166 )F0
26X-RAY DIFFRACTION26chain 'F' and (resid 167 through 233 )F0
27X-RAY DIFFRACTION27chain 'F' and (resid 234 through 268 )F0
28X-RAY DIFFRACTION28chain 'G' and (resid 13 through 42 )G0
29X-RAY DIFFRACTION29chain 'G' and (resid 43 through 105 )G0
30X-RAY DIFFRACTION30chain 'G' and (resid 106 through 184 )G0
31X-RAY DIFFRACTION31chain 'G' and (resid 185 through 268 )G0
32X-RAY DIFFRACTION32chain 'H' and (resid 13 through 91 )H0
33X-RAY DIFFRACTION33chain 'H' and (resid 92 through 184 )H0
34X-RAY DIFFRACTION34chain 'H' and (resid 185 through 268 )H0

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