[English] 日本語
Yorodumi
- PDB-4od4: Apo structure of a UbiA homolog from Aeropyrum pernix K1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4od4
TitleApo structure of a UbiA homolog from Aeropyrum pernix K1
Components4-hydroxybenzoate octaprenyltransferase
KeywordsTRANSFERASE / all alpha helical / intramembrane aromatic prenyltransferase / membrane
Function / homology
Function and homology information


Transferases; Transferring alkyl or aryl groups, other than methyl groups / transferase activity, transferring alkyl or aryl (other than methyl) groups / metal ion binding / plasma membrane
Similarity search - Function
UbiA prenyltransferase / UbiA prenyltransferase / 4-hydroxybenzoate polyprenyltransferase-related / Prenyltransferase / UbiA prenyltransferase family / UbiA prenyltransferase superfamily / UbiA prenyltransferase family / Tetracycline Repressor; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...UbiA prenyltransferase / UbiA prenyltransferase / 4-hydroxybenzoate polyprenyltransferase-related / Prenyltransferase / UbiA prenyltransferase family / UbiA prenyltransferase superfamily / UbiA prenyltransferase family / Tetracycline Repressor; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-hydroxybenzoate octaprenyltransferase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.301 Å
AuthorsLi, W. / Cheng, W.
CitationJournal: Science / Year: 2014
Title: Structural insights into ubiquinone biosynthesis in membranes.
Authors: Cheng, W. / Li, W.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 4-hydroxybenzoate octaprenyltransferase
B: 4-hydroxybenzoate octaprenyltransferase
C: 4-hydroxybenzoate octaprenyltransferase
D: 4-hydroxybenzoate octaprenyltransferase
E: 4-hydroxybenzoate octaprenyltransferase
F: 4-hydroxybenzoate octaprenyltransferase


Theoretical massNumber of molelcules
Total (without water)191,0196
Polymers191,0196
Non-polymers00
Water00
1
A: 4-hydroxybenzoate octaprenyltransferase


Theoretical massNumber of molelcules
Total (without water)31,8361
Polymers31,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-hydroxybenzoate octaprenyltransferase


Theoretical massNumber of molelcules
Total (without water)31,8361
Polymers31,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 4-hydroxybenzoate octaprenyltransferase


Theoretical massNumber of molelcules
Total (without water)31,8361
Polymers31,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 4-hydroxybenzoate octaprenyltransferase


Theoretical massNumber of molelcules
Total (without water)31,8361
Polymers31,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 4-hydroxybenzoate octaprenyltransferase


Theoretical massNumber of molelcules
Total (without water)31,8361
Polymers31,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 4-hydroxybenzoate octaprenyltransferase


Theoretical massNumber of molelcules
Total (without water)31,8361
Polymers31,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.090, 123.070, 423.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 3:277 ) and (not element H)
211chain 'B' and (resseq 3:277 ) and (not element H)
311chain 'C' and (resseq 3:277 ) and (not element H)
411chain 'D' and (resseq 3:277 ) and (not element H)
511chain 'E' and (resseq 3:277 ) and (not element H)
611chain 'F' and (resseq 3:277 ) and (not element H)

-
Components

#1: Protein
4-hydroxybenzoate octaprenyltransferase


Mass: 31836.461 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Gene: ubiA, APE_1570 / Production host: Escherichia coli (E. coli) / Strain (production host): C43
References: UniProt: Q9YBM8, Transferases; Transferring alkyl or aryl groups, other than methyl groups

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.78 Å3/Da / Density % sol: 74.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Na2SO4, 0.1M sodium cacodylate pH 5.0, 26.5% (w/v) PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9790, 0.97920, 0.96380
DetectorType: Pilatus detector / Detector: PIXEL / Date: Oct 22, 2012
RadiationMonochromator: Monochromator Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.96381
ReflectionResolution: 3.3→50 Å / Num. obs: 55984 / % possible obs: 99.4 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 6.8 % / Biso Wilson estimate: 108.4 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 14.1
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.892 / Mean I/σ(I) obs: 2.1 / Num. unique all: 5432 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
RAPDdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.301→49.783 Å / SU ML: 0.51 / σ(F): 1.35 / Phase error: 30.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3029 2824 5.05 %random
Rwork0.2715 ---
obs0.273 55886 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.301→49.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12036 0 0 0 12036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612300
X-RAY DIFFRACTIONf_angle_d0.8816854
X-RAY DIFFRACTIONf_dihedral_angle_d12.1964128
X-RAY DIFFRACTIONf_chiral_restr0.0322112
X-RAY DIFFRACTIONf_plane_restr0.0042076
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2006X-RAY DIFFRACTIONPOSITIONAL
12B2006X-RAY DIFFRACTIONPOSITIONAL0.022
13C2006X-RAY DIFFRACTIONPOSITIONAL0.022
14D2006X-RAY DIFFRACTIONPOSITIONAL0.019
15E2006X-RAY DIFFRACTIONPOSITIONAL0.023
16F2006X-RAY DIFFRACTIONPOSITIONAL0.02
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.301-3.35790.38881260.38372451X-RAY DIFFRACTION93
3.3579-3.4190.33751400.33342601X-RAY DIFFRACTION100
3.419-3.48470.31231400.29712660X-RAY DIFFRACTION100
3.4847-3.55580.36011410.29552614X-RAY DIFFRACTION100
3.5558-3.63310.31191320.29882637X-RAY DIFFRACTION100
3.6331-3.71760.32221340.28142677X-RAY DIFFRACTION100
3.7176-3.81060.30341410.26082598X-RAY DIFFRACTION100
3.8106-3.91360.29741590.25972639X-RAY DIFFRACTION100
3.9136-4.02870.31761360.26222610X-RAY DIFFRACTION99
4.0287-4.15860.28881480.25362618X-RAY DIFFRACTION98
4.1586-4.30720.26581410.23272619X-RAY DIFFRACTION100
4.3072-4.47950.28471580.24052645X-RAY DIFFRACTION100
4.4795-4.68330.29331510.25052691X-RAY DIFFRACTION100
4.6833-4.930.31571330.26942649X-RAY DIFFRACTION99
4.93-5.23850.31731470.26212668X-RAY DIFFRACTION100
5.2385-5.64250.28521290.26752650X-RAY DIFFRACTION98
5.6425-6.20940.32451670.28042687X-RAY DIFFRACTION100
6.2094-7.10570.29321240.24562735X-RAY DIFFRACTION100
7.1057-8.94390.21921360.2182744X-RAY DIFFRACTION99
8.9439-49.78860.33031410.32362869X-RAY DIFFRACTION98
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)
10.04320.15270.02560.55820.04130.0135-0.16750.0721-0.1461-0.2293-0.0076-0.36260.03820.3845-0.51770.05210.04990.16470.63870.09510.162977.834717.676685.7498
20.0475-0.0307-0.01440.01780.00210.03740.03790.0709-0.13840.03840.06420.0259-0.0198-0.00180.34550.04820.23270.05660.66730.05250.26156.998116.720995.5929
30.13310.0021-0.01960.0034-0.01780.0107-0.11010.1416-0.0673-0.018-0.1784-0.0184-0.06440.1086-1.0476-0.20490.08920.04371.17160.16970.414178.05567.620387.9285
40.2298-0.03210.02290.06660.12750.2851-0.071-0.15070.0070.1011-0.07540.07320.0406-0.084-0.01850.45250.26350.02641.38270.08980.750465.5416.1712110.2161
50.0751-0.013-0.00740.01430.0020.0049-0.09050.02390.0412-0.00890.01330.083-0.05060.0702-0.1689-0.21480.0279-0.15160.81670.130.30590.448811.3841101.7775
60.08150.0345-0.03160.0223-0.02140.04270.05990.01370.0298-0.03780.00030.0441-0.0115-0.06040.1983-0.0727-0.29160.09320.8259-0.28090.400384.428620.6743103.7244
70.07150.0423-0.00390.03530.02760.4501-0.1202-0.1054-0.02720.02430.00560.0677-0.0388-0.2385-0.43790.67010.22760.05950.39990.06390.01863.667325.569964.4667
80.0853-0.0201-0.07530.07160.03860.0763-0.0575-0.0871-0.0782-0.26560.019-0.23090.01090.42790.21540.85150.38790.13341.65420.29680.496275.20768.468354.1436
90.1081-0.1181-0.00140.0769-0.03720.0095-0.11640.02380.04530.02640.0217-0.01040.18440.2824-0.83920.13520.4665-0.00170.43520.24330.124156.088519.187155.6307
100.0485-0.07160.09740.1188-0.16290.22260.014-0.0070.08390.01860.02970.0099-0.23570.0241-0.03251.11770.47690.10571.0172-0.03880.486450.808840.211954.4526
110.50330.1645-0.04450.6817-0.10440.0198-0.037-0.35320.15230.43710.042-0.1356-0.19980.00030.15620.38640.1408-0.04320.221-0.05420.377962.818633.506846.816
120.1846-0.08080.13190.1689-0.3180.59270.09530.0967-0.253-0.1745-0.00990.03780.3426-0.02370.0630.64260.1544-0.12790.09880.105-0.084450.248141.851515.8121
130.01110.02610.02510.08040.06030.0448-0.0041-0.1150.11630.51380.11240.1154-0.4283-0.22260.07670.83650.35010.0170.35530.07140.208545.569151.883515.046
140.0066-0.02180.01450.0333-0.01120.03960.03410.04560.0172-0.011-0.03710.0168-0.0650.01470.03711.3040.0897-0.1539-0.0632-0.01520.000540.793165.742125.9601
150.1956-0.11850.22870.1099-0.15670.2757-0.1385-0.3055-0.0394-0.00450.31980.2636-0.4042-0.34150.15951.23870.6929-0.02220.44590.4010.448838.507143.238817.3988
160.038-0.0342-0.00240.0789-0.02230.0193-0.0014-0.1812-0.0449-0.00750.10970.0585-0.0873-0.21260.05191.35490.49880.06471.04310.23690.534333.121653.883440.0531
170.2652-0.01660.14110.0102-0.02690.08360.17760.0325-0.2294-0.03550.21760.30860.0127-0.09921.41470.85830.30410.02490.4050.15970.500446.647634.424234.1857
180.10270.0464-0.00810.0605-0.00550.0116-0.0451-0.15610.17140.19160.16410.3827-0.2284-0.1505-0.0230.80850.2302-0.00310.3942-0.01260.539955.149140.893627.8977
190.75160.04640.05370.26930.00990.0124-0.07180.215-0.0686-0.2522-0.0249-0.3669-0.17770.3135-0.28580.26170.18830.12520.9314-0.02680.438136.146783.92375.3436
200.0219-0.01150.0020.2266-0.05640.08070.2180.3416-0.1348-0.3572-0.29630.05360.12280.0676-0.08340.38550.4079-0.01281.3132-0.02240.576822.969478.977176.4248
210.8513-0.02980.08370.54960.02420.02420.11550.3926-0.1155-0.3089-0.0735-0.3737-0.00590.45090.61390.17310.39440.13341.10210.16350.488837.843472.63879.8835
220.3392-0.164-0.15020.11980.130.1848-0.0524-0.0229-0.1170.0153-0.05480.0610.05020.0051-0.15950.31390.26940.12150.73440.20920.609923.697468.723597.6184
230.4704-0.20590.04940.2260.00780.01420.0311-0.29230.2882-0.02640.1298-0.2052-0.05540.24120.41360.02110.02380.07811.4043-0.0390.730244.841881.264292.6368
240.01530.08350.01680.59290.12560.0289-0.1389-0.29490.0141-0.0277-0.03060.3423-0.0397-0.2499-0.36240.52910.4506-0.04230.49760.05120.186518.748496.377653.2675
250.00590.00330.00070.0349-0.02340.0134-0.00670.04620.002-0.1705-0.0585-0.02610.10290.0849-0.22490.75560.522-0.0680.4216-0.10750.139925.065287.278453.8555
260.30260.25880.11830.30890.17520.1143-0.13860.23820.0535-0.39420.1908-0.01340.10090.1620.24331.67310.86160.37051.78110.53030.763435.738577.165742.9979
270.3354-0.2440.30530.8073-0.42330.53610.28610.1571-0.2885-0.55620.0428-0.05850.36680.00890.56160.84250.411-0.26130.29750.21430.280514.580384.079353.3966
280.28350.00890.21540.148-0.10790.2330.20980.3441-0.0433-0.5218-0.05860.36180.44460.29980.27771.70490.6487-0.13090.7280.00830.72414.171890.858235.6265
290.0707-0.0688-0.02370.10470.06920.062-0.0593-0.103-0.2037-0.31950.0177-0.12620.16170.0173-0.08940.97050.54090.26680.3164-0.16050.297420.3699100.643136.1908
300.42280.28720.06650.60080.36790.302-0.06250.3884-0.2855-0.08430.2044-0.15780.22390.07110.23441.09230.30870.22460.677-0.27480.103317.7429115.89775.9799
310.1130.2083-0.13940.3829-0.2570.17470.02440.1160.05180.03470.1310.0822-0.24020.21260.10860.77830.072-0.03040.7098-0.04110.187811.0774124.74685.2616
320.17130.04050.07240.03840.04140.0562-0.0099-0.38530.2988-0.0619-0.05940.1071-0.37690.01420.15331.117-0.1193-0.19970.60110.020.49583.3057137.089816.2738
330.0537-0.06410.0170.0883-0.02020.00790.07150.0324-0.0136-0.2442-0.03320.01340.08890.03250.07861.5473-0.1615-0.11950.3084-0.03820.42366.8195118.9069-3.5104
340.0661-0.08070.07440.4574-0.31210.21770.07480.1464-0.0909-0.30690.1970.18550.2289-0.0820.48060.8358-0.0924-0.18890.09260.14060.3382.347117.893312.3754
350.1633-0.04240.01050.0188-0.00790.0008-0.08390.154-0.251-0.2680.0564-0.00930.1731-0.00310.01121.38370.27660.14170.4614-0.04690.40899.0614108.86589.261
360.08820.05360.11040.04940.04270.1980.0903-0.1953-0.10830.02510.02380.0561-0.0644-0.21550.08720.67370.1498-0.05990.4270.15780.3708-1.9487123.621630.0284
370.4903-0.32740.1450.74040.03630.29040.24660.4415-0.0629-0.24880.1458-0.01850.30710.36911.78941.16940.91910.00470.55190.07960.484317.7365110.178422.2223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 178 )
4X-RAY DIFFRACTION4chain 'A' and (resid 179 through 198 )
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 238 )
6X-RAY DIFFRACTION6chain 'A' and (resid 239 through 277 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 53 )
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 85 )
9X-RAY DIFFRACTION9chain 'B' and (resid 86 through 218 )
10X-RAY DIFFRACTION10chain 'B' and (resid 219 through 238 )
11X-RAY DIFFRACTION11chain 'B' and (resid 239 through 277 )
12X-RAY DIFFRACTION12chain 'C' and (resid 3 through 28 )
13X-RAY DIFFRACTION13chain 'C' and (resid 29 through 53 )
14X-RAY DIFFRACTION14chain 'C' and (resid 54 through 85 )
15X-RAY DIFFRACTION15chain 'C' and (resid 86 through 178 )
16X-RAY DIFFRACTION16chain 'C' and (resid 179 through 198 )
17X-RAY DIFFRACTION17chain 'C' and (resid 199 through 253 )
18X-RAY DIFFRACTION18chain 'C' and (resid 254 through 277 )
19X-RAY DIFFRACTION19chain 'D' and (resid 3 through 53 )
20X-RAY DIFFRACTION20chain 'D' and (resid 54 through 108 )
21X-RAY DIFFRACTION21chain 'D' and (resid 109 through 178 )
22X-RAY DIFFRACTION22chain 'D' and (resid 179 through 198 )
23X-RAY DIFFRACTION23chain 'D' and (resid 199 through 277 )
24X-RAY DIFFRACTION24chain 'E' and (resid 3 through 28 )
25X-RAY DIFFRACTION25chain 'E' and (resid 29 through 53 )
26X-RAY DIFFRACTION26chain 'E' and (resid 54 through 85 )
27X-RAY DIFFRACTION27chain 'E' and (resid 86 through 158 )
28X-RAY DIFFRACTION28chain 'E' and (resid 159 through 238 )
29X-RAY DIFFRACTION29chain 'E' and (resid 239 through 277 )
30X-RAY DIFFRACTION30chain 'F' and (resid 3 through 28 )
31X-RAY DIFFRACTION31chain 'F' and (resid 29 through 53 )
32X-RAY DIFFRACTION32chain 'F' and (resid 54 through 85 )
33X-RAY DIFFRACTION33chain 'F' and (resid 86 through 108 )
34X-RAY DIFFRACTION34chain 'F' and (resid 109 through 144 )
35X-RAY DIFFRACTION35chain 'F' and (resid 145 through 178 )
36X-RAY DIFFRACTION36chain 'F' and (resid 179 through 198 )
37X-RAY DIFFRACTION37chain 'F' and (resid 199 through 277 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • 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

-
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

Read more