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- PDB-4q3o: Crystal structure of MGS-MT1, an alpha/beta hydrolase enzyme from... -

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Basic information

Entry
Database: PDB / ID: 4q3o
TitleCrystal structure of MGS-MT1, an alpha/beta hydrolase enzyme from a Lake Matapan deep-sea metagenome library
ComponentsMGS-MT1
KeywordsHYDROLASE / metagenome / metagenomic library / alpha and beta proteins / alpha/beta hydrolase superfamily / esterase/lipase fold
Function / homologyAlpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / hydrolase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Carboxylesterase
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsStogios, P.J. / Xu, X. / Cui, H. / Alcaide, M. / Ferrer, M. / Savchenko, A.
CitationJournal: Environ Microbiol / Year: 2015
Title: Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats.
Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / ...Authors: Alcaide, M. / Stogios, P.J. / Lafraya, A. / Tchigvintsev, A. / Flick, R. / Bargiela, R. / Chernikova, T.N. / Reva, O.N. / Hai, T. / Leggewie, C.C. / Katzke, N. / La Cono, V. / Matesanz, R. / Jebbar, M. / Jaeger, K.E. / Yakimov, M.M. / Yakunin, A.F. / Golyshin, P.N. / Golyshina, O.V. / Savchenko, A. / Ferrer, M.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Sep 20, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: MGS-MT1
B: MGS-MT1
C: MGS-MT1
D: MGS-MT1
E: MGS-MT1
F: MGS-MT1
G: MGS-MT1
H: MGS-MT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,39245
Polymers307,5208
Non-polymers3,87237
Water55,5763085
1
A: MGS-MT1
B: MGS-MT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,94012
Polymers76,8802
Non-polymers1,06010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-34 kcal/mol
Surface area23400 Å2
MethodPISA
2
C: MGS-MT1
F: MGS-MT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,83712
Polymers76,8802
Non-polymers95710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-36 kcal/mol
Surface area23370 Å2
MethodPISA
3
D: MGS-MT1
G: MGS-MT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,08913
Polymers76,8802
Non-polymers1,20911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-23 kcal/mol
Surface area23110 Å2
MethodPISA
4
E: MGS-MT1
H: MGS-MT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5258
Polymers76,8802
Non-polymers6466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-28 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.454, 131.397, 112.441
Angle α, β, γ (deg.)90.00, 103.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

21A-700-

HOH

31H-714-

HOH

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Components

#1: Protein
MGS-MT1


Mass: 38439.945 Da / Num. of mol.: 8 / Fragment: MGS-MT1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Gene: MGS-MT1 / Plasmid: p15Tv-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: A0A0B5KQQ5*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3085 / Source method: isolated from a natural source / Formula: H2O
Source detailsThe sample has been obtained from Lake Matapan deep-sea and identified using the technique metagenome library

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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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES, 20% PEG10K. Cryroprotectant: 12% Glycerol then paraton-N oil, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 10, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→19.72 Å / Num. obs: 272067 / Observed criterion σ(F): -2 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.3
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.9pre_1669)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FAK
Resolution: 1.74→19.72 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1852 13720 5.05 %
Rwork0.1452 --
obs0.1472 271731 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19746 0 232 3085 23063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01520641
X-RAY DIFFRACTIONf_angle_d1.48228138
X-RAY DIFFRACTIONf_dihedral_angle_d14.0747600
X-RAY DIFFRACTIONf_chiral_restr0.0833172
X-RAY DIFFRACTIONf_plane_restr0.0083572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.75980.25054620.20288611X-RAY DIFFRACTION100
1.7598-1.78040.2534480.28621X-RAY DIFFRACTION100
1.7804-1.80210.22924710.18838637X-RAY DIFFRACTION100
1.8021-1.82490.22564370.18398608X-RAY DIFFRACTION100
1.8249-1.84890.24145000.18198557X-RAY DIFFRACTION100
1.8489-1.87430.2344530.18338655X-RAY DIFFRACTION100
1.8743-1.9010.23544400.18228600X-RAY DIFFRACTION100
1.901-1.92940.23354650.19038599X-RAY DIFFRACTION100
1.9294-1.95950.2154910.16378553X-RAY DIFFRACTION100
1.9595-1.99160.19124320.15128631X-RAY DIFFRACTION100
1.9916-2.02590.19134850.14698625X-RAY DIFFRACTION100
2.0259-2.06270.1994510.15558617X-RAY DIFFRACTION100
2.0627-2.10230.19584510.14838591X-RAY DIFFRACTION100
2.1023-2.14520.18764590.13438598X-RAY DIFFRACTION100
2.1452-2.19180.17024530.13368660X-RAY DIFFRACTION100
2.1918-2.24270.19624470.14568597X-RAY DIFFRACTION100
2.2427-2.29870.22574490.15828667X-RAY DIFFRACTION100
2.2987-2.36070.17844840.13438539X-RAY DIFFRACTION100
2.3607-2.43010.1724690.13368648X-RAY DIFFRACTION100
2.4301-2.50840.19154400.13318675X-RAY DIFFRACTION100
2.5084-2.59780.19114700.13748578X-RAY DIFFRACTION100
2.5978-2.70160.18694580.13858657X-RAY DIFFRACTION100
2.7016-2.82420.18334630.13138633X-RAY DIFFRACTION100
2.8242-2.97260.17474590.13698673X-RAY DIFFRACTION100
2.9726-3.15820.17824290.13698640X-RAY DIFFRACTION100
3.1582-3.40090.16614710.13158638X-RAY DIFFRACTION100
3.4009-3.7410.154420.12388620X-RAY DIFFRACTION99
3.741-4.27750.1524430.11978566X-RAY DIFFRACTION99
4.2775-5.37120.15584580.13568454X-RAY DIFFRACTION97
5.3712-19.72490.20434400.18538263X-RAY DIFFRACTION94
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)
12.8078-1.2582-1.42643.84535.18967.16320.0802-0.2993-0.47470.4954-0.31310.24451.0117-0.46260.19610.367-0.06490.01950.22560.10370.212727.3325-23.082525.7834
22.4658-0.33170.24652.40470.55881.8751-0.0695-0.020.02950.0545-0.00980.1850.0488-0.30790.05190.0654-0.03040.00270.1740.00130.140212.1756-10.72776.593
30.9946-0.03770.2620.77310.05951.15310.0002-0.00250.01490.0130.02730.02650.0604-0.062-0.02260.0604-0.01750.00440.08320.00560.088929.2352-11.49788.2625
47.45491.9792-5.96746.5248-4.92728.0008-0.1506-0.46180.55740.4082-0.1037-0.1289-0.64970.20070.14690.21520.0352-0.07620.1587-0.10290.215922.29194.97515.3028
57.80841.56581.76529.0047-2.1865.89650.1701-0.3152-0.50610.4826-0.1146-0.24430.43450.26960.0120.18810.04720.01490.1297-0.02360.137451.2308-17.897710.3426
64.42254.90613.916.09554.54023.5530.0056-0.1412-0.2221-0.1858-0.0046-0.1232-0.0318-0.10180.06690.14910.01640.00080.11080.0030.150457.391-20.576634.5862
70.59441.3356-1.14277.613-6.76445.9697-0.01880.0359-0.1326-0.0007-0.1339-0.34110.07570.17780.27720.1250.025-0.04980.1185-0.03380.202566.6093-5.947526.2656
80.86570.30410.09750.63080.04430.7134-0.0021-0.07830.09860.0673-0.02190.039-0.0965-0.04980.01620.09730.0139-0.0060.0754-0.0210.083649.10782.217125.9104
97.98312.3953-0.18318.66361.05634.6490.0282-0.48-0.35230.4356-0.096-0.30660.37440.3310.050.1190.0280.03060.1436-0.01070.115417.5195-50.2268-44.4056
103.67524.88154.33257.07035.90895.1446-0.0181-0.0631-0.1887-0.2040.1013-0.34520.080.0549-0.0880.1890.05190.0170.1572-0.00760.207621.3237-55.4539-21.3948
110.14480.5333-0.52947.0555-6.70786.318-0.1289-0.0275-0.11120.2037-0.1795-0.6146-0.17770.22580.42560.14320.0289-0.04070.1431-0.04490.241630.7293-38.8408-27.6899
120.81820.22180.13260.6922-0.03610.9536-0.0275-0.13490.10590.1225-0.00830.0015-0.1281-0.09190.0140.11680.0362-0.00490.1051-0.03960.101412.9913-31.8589-27.82
137.00130.4213-0.91988.8552-2.7477.9724-0.0641-0.2989-0.46570.4624-0.086-0.27760.4520.46380.08090.17820.0518-0.01010.1124-0.03260.207718.27615.9307-44.7719
140.04240.1819-0.10623.0435-2.82042.61480.0161-0.0401-0.1268-0.03-0.0632-0.11530.04720.11050.0840.15040.0362-0.00740.11270.00310.217130.235822.7772-27.2957
150.97840.42570.30120.64950.00680.72620.0545-0.17290.0490.0829-0.070.0679-0.0244-0.10580.00720.10470.0024-0.00190.095-0.0160.09715.123334.2089-26.5154
164.1339-3.3658-1.70295.44812.85533.91650.06150.17030.127-0.1648-0.1287-0.0403-0.1473-0.17830.05690.0929-0.0281-0.03240.05980.00470.117714.272635.1487-42.0051
178.3786-0.2731-0.77377.18673.91948.8409-0.13920.3331-0.3299-0.2826-0.1010.24350.5083-0.29380.17580.177-0.0230.03670.12140.03150.098242.2824-17.0279-9.4698
185.5945-3.03185.49244.5036-4.90968.07620.351-0.0521-0.22730.1898-0.06260.22640.13580.0437-0.23520.2773-0.04860.00490.2129-0.03460.300536.8598-22.4827-32.3477
190.4336-0.1585-0.11456.24742.28961.9741-0.07210.0216-0.1375-0.1809-0.1330.40510.0177-0.18570.32540.0568-0.0234-0.02030.10880.01730.223128.9605-5.7032-26.7958
200.8019-0.25140.03450.89660.13251.20830.01430.15710.1009-0.1416-0.0274-0.0101-0.08820.1603-0.00110.1107-0.0224-0.00040.13030.03780.094347.23480.2607-27.2975
211.2282-1.6989-2.21734.98176.20828.0456-0.0281-0.2089-0.39250.5963-0.17230.23140.9568-0.5350.26660.3254-0.05360.04760.32970.08450.211-7.4628-57.5098-29.2331
227.3712-1.9179-3.61387.42255.31297.910.1273-0.0899-0.97350.40190.24080.03520.2669-0.3332-0.09290.2373-0.06110.01980.41860.19690.4212-21.4679-60.3979-44.2188
231.7927-0.2204-0.24132.29030.44291.3944-0.0532-0.06240.1059-0.04930.04440.2602-0.0794-0.33120.01480.07190.00930.00970.21660.00710.1554-22.147-41.7543-50.8386
240.8394-0.04180.23560.6518-0.15591.069-0.0214-0.1047-0.00080.07330.0190.058-0.0262-0.13750.00820.0602-0.0070.02120.1169-0.00830.0804-5.8219-44.6958-46.2292
250.33450.0720.15483.31682.17741.4710.1437-0.3565-0.41580.2406-0.1576-0.02430.6698-0.27290.02240.4284-0.1569-0.03990.30630.09290.3297-5.48088.4193-28.0382
262.8005-2.1694-1.96385.68452.27772.3020.0995-0.1297-0.61810.6469-0.21890.38140.3088-0.32020.04070.4383-0.2049-0.00990.41790.01520.3905-20.76026.6318-41.68
271.3786-0.1204-0.1081.97420.59731.61210.01540.02970.00730.0076-0.15530.2383-0.0111-0.4639-0.01710.093-0.02070.0040.2564-0.03980.1537-21.788324.0876-48.528
281.045-0.09160.25960.77950.01361.19540.0307-0.0801-0.07110.064-0.0058-0.02910.0559-0.1347-0.03810.0768-0.0315-0.00510.1017-0.00540.1072-5.177921.4429-44.9953
294.12572.3928-3.6566.3564-3.63395.1564-0.0958-0.0167-0.54-0.0367-0.3139-0.33110.73350.5750.40820.37660.14850.00940.3255-0.08020.216766.0903-27.4711-24.7844
307.63871.3537-2.28724.1364-0.55923.9181-0.04620.0172-1.0013-0.3167-0.1003-0.45020.57160.29510.17010.36810.2187-0.01320.4322-0.03890.439879.6419-31.1396-10.0252
312.10410.1856-0.50012.8122-0.70951.5738-0.0359-0.0280.07620.0662-0.0682-0.4314-0.00360.48980.08480.13380.0325-0.00210.34420.01210.217482.548-11.7464-5.7687
320.8321-0.06560.21760.7762-0.01741.1704-0.01130.0507-0.0248-0.01670.026-0.08840.09440.2189-0.01120.11740.0560.00890.2052-0.00990.108465.8388-13.2111-9.0775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( chain A and resid 31:60 )A31 - 60
2X-RAY DIFFRACTION2( chain A and resid 61:189 )A61 - 189
3X-RAY DIFFRACTION3( chain A and resid 190:336 )A190 - 336
4X-RAY DIFFRACTION4( chain A and resid 337:347 )A337 - 347
5X-RAY DIFFRACTION5( chain B and resid 31:51 )B31 - 51
6X-RAY DIFFRACTION6( chain B and resid 52:67 )B52 - 67
7X-RAY DIFFRACTION7( chain B and resid 68:88 )B68 - 88
8X-RAY DIFFRACTION8( chain B and resid 89:347 )B89 - 347
9X-RAY DIFFRACTION9( chain C and resid 32:51 )C32 - 51
10X-RAY DIFFRACTION10( chain C and resid 52:64 )C52 - 64
11X-RAY DIFFRACTION11( chain C and resid 65:91 )C65 - 91
12X-RAY DIFFRACTION12( chain C and resid 92:347 )C92 - 347
13X-RAY DIFFRACTION13( chain D and resid 32:51 )D32 - 51
14X-RAY DIFFRACTION14( chain D and resid 52:90 )D52 - 90
15X-RAY DIFFRACTION15( chain D and resid 91:323 )D91 - 323
16X-RAY DIFFRACTION16( chain D and resid 324:347 )D324 - 347
17X-RAY DIFFRACTION17( chain E and resid 32:50 )E32 - 50
18X-RAY DIFFRACTION18( chain E and resid 51:65 )E51 - 65
19X-RAY DIFFRACTION19( chain E and resid 66:90 )E66 - 90
20X-RAY DIFFRACTION20( chain E and resid 91:347 )E91 - 347
21X-RAY DIFFRACTION21( chain F and resid 32:59 )F32 - 59
22X-RAY DIFFRACTION22( chain F and resid 60:89 )F60 - 89
23X-RAY DIFFRACTION23( chain F and resid 90:189 )F90 - 189
24X-RAY DIFFRACTION24( chain F and resid 190:347 )F190 - 347
25X-RAY DIFFRACTION25( chain G and resid 32:59 )G32 - 59
26X-RAY DIFFRACTION26( chain G and resid 60:91 )G60 - 91
27X-RAY DIFFRACTION27( chain G and resid 92:189 )G92 - 189
28X-RAY DIFFRACTION28( chain G and resid 190:347 )G190 - 347
29X-RAY DIFFRACTION29( chain H and resid 32:60 )H32 - 60
30X-RAY DIFFRACTION30( chain H and resid 61:87 )H61 - 87
31X-RAY DIFFRACTION31( chain H and resid 88:189 )H88 - 189
32X-RAY DIFFRACTION32( chain H and resid 190:347 )H190 - 347

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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

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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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