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- PDB-5u2w: Crystal structure of a Short chain dehydrogenase from Burkholderi... -

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Basic information

Entry
Database: PDB / ID: 5u2w
TitleCrystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


: / nucleotide binding
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short chain dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionDec 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Short chain dehydrogenase
B: Short chain dehydrogenase
C: Short chain dehydrogenase
D: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,82320
Polymers104,0774
Non-polymers3,74716
Water22,6271256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20650 Å2
ΔGint-12 kcal/mol
Surface area29760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.970, 72.370, 100.530
Angle α, β, γ (deg.)90.000, 100.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-407-

HOH

21C-535-

HOH

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Components

#1: Protein
Short chain dehydrogenase


Mass: 26019.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAL2464 / Plasmid: BuceA.00010.g.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4E730
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1256 / 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: 2.35 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Molecular Dimensions Morpheus screen G2: 10% w/v PEG 8000, 20% v/v ethylene glycol: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium ...Details: Molecular Dimensions Morpheus screen G2: 10% w/v PEG 8000, 20% v/v ethylene glycol: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate: 100mM MES/imidazole pH 6.5: BuceA.00010.g.B1.PW37236 at 20.78mg/ml + 4mM NADP: cryo: direct: tray 285571g2, puck yrq2-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→43.945 Å / Num. obs: 137073 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 14.301 % / Biso Wilson estimate: 10.88 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Net I/σ(I): 38.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2% possible all
1.55-1.598.3090.396.01126230.91190.4
1.59-1.6310.3560.327.640.95194
1.63-1.6811.2940.2668.980.9795.5
1.68-1.7311.6340.22210.770.98196.7
1.73-1.7912.0320.19112.530.98898
1.79-1.8512.4450.15715.030.99298.8
1.85-1.9212.8760.12119.080.99699.6
1.92-213.2910.10224.040.99799.9
2-2.0913.8780.08130.060.99899.9
2.09-2.1914.3360.06438.680.999100
2.19-2.3113.1580.06742.50.99999.8
2.31-2.4515.0250.05349.930.99999.8
2.45-2.6214.130.05454.370.99999.8
2.62-2.8316.2520.04263.991100
2.83-3.117.5320.03575.25199.9
3.1-3.4718.2120.03586.751100
3.47-423.1090.027113.33199.9
4-4.929.0390.025137.29199.8
4.9-6.9329.480.026127.621100
6.93-43.94527.9220.022139.720.99999.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXmodel building
Cootmodel building
PHENIX(dev_2597)refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3v2g via Balbes
Resolution: 1.55→43.945 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.22
RfactorNum. reflection% reflection
Rfree0.1632 2019 1.47 %
Rwork0.1369 --
obs0.1373 137043 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.99 Å2 / Biso mean: 15.5888 Å2 / Biso min: 4.38 Å2
Refinement stepCycle: final / Resolution: 1.55→43.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6919 0 244 1314 8477
Biso mean--12.98 28.64 -
Num. residues----981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087512
X-RAY DIFFRACTIONf_angle_d1.01710261
X-RAY DIFFRACTIONf_chiral_restr0.0641206
X-RAY DIFFRACTIONf_plane_restr0.0061454
X-RAY DIFFRACTIONf_dihedral_angle_d12.9514622
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.58880.24141270.18648807893490
1.5888-1.63170.19221520.1569173932594
1.6317-1.67970.17141360.14799375951195
1.6797-1.7340.19141460.14339475962197
1.734-1.79590.16181230.13899642976598
1.7959-1.86780.15371370.13859658979599
1.8678-1.95290.18191480.139298179965100
1.9529-2.05580.17741580.13897799937100
2.0558-2.18460.1361380.12998379975100
2.1846-2.35330.13391450.130698289973100
2.3533-2.59010.18231580.136298359993100
2.5901-2.96480.16921550.1372984810003100
2.9648-3.7350.15871480.1304989410042100
3.735-43.96290.14491480.13191005610204100
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)
12.4319-0.19430.25854.9011-0.93263.0259-0.0180.45410.0571-0.276-0.0320.0549-0.1293-0.07240.02250.0658-0.00370.02770.14390.00150.054949.14093.81211.3809
22.5790.27120.19851.51810.25222.3267-0.07840.1835-0.0818-0.05440.051-0.05960.0210.03770.01250.06030.0020.03380.0732-0.02060.069151.6608-1.76363.5201
31.22210.09050.68551.48951.33645.2645-0.00820.2601-0.1336-0.19940.0577-0.1345-0.08240.3262-0.03470.08140.00770.03930.1499-0.01750.133558.5004-1.09382.5199
44.058-1.89173.12433.8909-4.2777.2854-0.0930.06880.21880.1254-0.1541-0.3709-0.40570.510.1450.0677-0.0230.01030.0971-0.00050.12159.42510.05299.9047
50.9127-0.51970.19982.0486-2.35844.6905-0.0454-0.1128-0.1192-0.0344-0.0088-0.09720.25630.21560.04630.06160.02040.00220.068200.101751.8892-3.780622.7772
60.747-0.0784-0.02621.0497-0.68181.2688-0.005-0.00930.0527-0.03090.01870.03420.00590.0099-0.0090.0422-0.0017-0.00270.0419-0.01310.047243.6454.488118.666
71.3165-0.6958-0.08073.88530.50350.4876-0.0543-0.0092-0.25080.07090.0278-0.1570.14010.09970.00240.09020.01390.01620.061-0.00040.114143.3673-8.516213.6982
81.06490.7657-0.76223.6574-1.81562.0088-0.10240.0247-0.2159-0.10690.0706-0.12820.23580.04090.03540.08080.002-0.00270.0635-0.01940.093137.5066-13.022610.4636
91.46510.01430.17330.23050.21971.1266-0.00290.06570.0888-0.08930.0095-0.0123-0.0270.0520.00080.0442-0.00540.00320.0529-0.01390.059334.14891.178310.4504
102.30970.9235-0.02215.7917-0.8091.6510.0366-0.406-0.12150.2130.05970.21460.125-0.215-0.08550.1142-0.0128-0.02050.22590.02030.063439.23370.451553.0192
112.18450.03090.15310.9853-0.18871.7697-0.0741-0.26230.06170.0160.08380.0171-0.0097-0.0962-0.01770.09850.0244-0.00620.1483-0.03010.047640.88526.411251.9754
120.7883-0.449-0.38720.78620.93472.2152-0.0757-0.22990.05270.12520.1123-0.03050.07330.1282-0.03460.11080.0182-0.01130.164-0.03340.090946.49896.998455.7295
136.11822.1018-3.97821.9256-1.5192.849-0.1023-0.3846-0.13390.05490.0498-0.16080.33860.33940.07670.0940.033-0.02840.1729-0.020.097252.8763-3.77549.5177
141.00170.5662-0.46671.9686-1.50633.2242-0.0131-0.00530.0398-0.00030.0335-0.065-0.12010.1195-0.00530.0588-0.0093-0.02140.0861-0.02860.07148.50784.650836.241
150.9695-0.8040.8532.5514-2.64173.86570.0336-0.0749-0.037-0.02520.12560.1475-0.0002-0.1441-0.16490.05290.0021-0.00590.0647-0.01140.054436.80082.716535.5873
160.9716-0.04120.10140.19520.25680.7491-0.0241-0.08590.04630.04120.016-0.0071-0.05320.02460.00890.06840.0066-0.01040.0781-0.0050.054238.2833.303136.0496
170.6018-0.41620.6133.1412-2.20112.6903-0.0742-0.08210.11680.0680.0214-0.0536-0.2256-0.01220.04090.10320.0221-0.00610.1193-0.04350.091628.46914.153739.5778
180.6574-0.53270.42293.8476-1.15780.82720.0048-0.1538-0.01550.12770.0258-0.04210.0033-0.047-0.03920.06190.0102-0.00530.1-0.00140.049828.19850.318838.6809
192.7627-0.7633-0.28014.97610.70192.1706-0.01960.337-0.1325-0.1884-0.06770.00190.04960.09440.03950.0594-0.0068-0.01710.09540.00340.016419.4902-4.1425-4.2471
203.1355-0.0111-0.16511.56670.15151.7532-0.04260.11860.0265-0.04890.0015-0.0241-0.0339-0.01520.02810.0665-0.0065-0.01180.05190.01430.022916.63521.3852-3.7296
213.4066-3.3446-3.90425.2132.07176.46630.06040.34890.1499-0.3174-0.0703-0.0984-0.1929-0.0764-0.03440.1372-0.0259-0.04470.1390.04480.095813.33993.8863-11.1925
222.0280.0449-1.991.2243-0.14144.57140.01390.10070.0632-0.15310.0351-0.0065-0.010.0301-0.03090.0655-0.0083-0.0240.0764-0.00410.04959.6665-2.8723-4.3187
234.4829-2.893-4.9642.66163.11715.5008-0.13570.1589-0.19150.0081-0.01140.16180.2851-0.24510.20380.0759-0.0063-0.01270.0958-0.00490.09756.8592-10.5967-0.0454
241.3572-0.7196-0.61361.67651.10412.6753-0.0149-0.04770.08640.03650.04660.0144-0.107-0.1322-0.02380.0380.0059-0.01640.05790.01270.05749.43990.351312.4206
250.90440.20270.19771.42681.22971.8180.0123-0.0120.03840.00250.1071-0.1456-0.07340.0976-0.10030.05910.0051-0.01020.03940.00670.060820.9190.294213.106
261.1073-1.0716-0.31272.4390.84620.7980.0123-0.0207-0.04840.02250.0118-0.0430.0327-0.0307-0.01890.0558-0.0086-0.00640.05470.01160.042518.207-4.424217.0474
271.4837-0.6852-0.25413.891-0.27951.7227-0.00150.0362-0.134-0.18510.04260.18420.1618-0.0670.01220.063-0.01-0.01490.0320.00120.063923.6673-8.72669.8113
283.26150.29991.09147.4366-0.88850.4991-0.2089-0.17410.71180.11040.01580.4089-0.2296-0.28620.12810.15740.0165-0.050.0961-0.01380.202618.11417.08177.6681
290.7823-0.01930.50383.94272.06452.3616-0.08740.0360.1518-0.13250.01930.0932-0.241-0.02420.05760.082-0.0186-0.00210.07170.02030.092227.194612.79697.7972
300.81130.2670.28962.52680.85940.883-0.01020.0769-0.0319-0.09770.0449-0.00010.00620.0386-0.04510.0636-0.0114-0.00310.05820.00010.063630.14-0.76379.9859
312.36910.3278-0.09015.83830.90982.05880.1031-0.30930.19780.329-0.0337-0.0461-0.107-0.0627-0.06870.09730.00910.03150.1923-0.00920.07078.10941.00645.938
320.99170.2983-0.21171.2539-0.22321.124-0.0136-0.32960.00420.13320.02250.1375-0.012-0.0598-0.01710.09910.01830.0290.19090.03130.09074.9918-6.438246.9782
331.15310.4142-0.09831.97790.97834.7949-0.0142-0.19750.19940.10170.04870.2965-0.1408-0.26350.00860.07770.03930.04420.21860.02140.1658-1.54341.960239.9832
341.0796-0.2858-0.31491.18580.60971.6089-0.0163-0.0514-0.01810.05550.04210.09170.0539-0.1363-0.01040.0579-0.00830.00970.0850.03420.068810.4241-3.338328.8919
350.75390.0301-0.0630.1392-0.18470.888-0.0331-0.0966-0.07490.02610.02230.04740.0378-0.08410.00790.0480.00690.01010.08820.01510.063615.9881-2.430731.52
361.5433-1.6174-1.13763.73251.90141.9326-0.1166-0.1498-0.17930.14740.07220.14590.1931-0.02120.05850.0734-0.0033-0.00650.12110.04410.076823.418-12.932739.1957
371.8855-0.4430.09281.0533-0.69390.61550.0036-0.15760.05990.0508-0.02440.0765-0.0966-0.05490.01290.05930.00230.00130.10510.00450.043224.07691.391738.1462
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )A1 - 16
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 40 )A17 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 67 )A41 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 82 )A68 - 82
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 116 )A83 - 116
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 176 )A117 - 176
7X-RAY DIFFRACTION7chain 'A' and (resid 177 through 199 )A177 - 199
8X-RAY DIFFRACTION8chain 'A' and (resid 200 through 225 )A200 - 225
9X-RAY DIFFRACTION9chain 'A' and (resid 226 through 246 )A226 - 246
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 16 )B2 - 16
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 40 )B17 - 40
12X-RAY DIFFRACTION12chain 'B' and (resid 41 through 67 )B41 - 67
13X-RAY DIFFRACTION13chain 'B' and (resid 68 through 82 )B68 - 82
14X-RAY DIFFRACTION14chain 'B' and (resid 83 through 128 )B83 - 128
15X-RAY DIFFRACTION15chain 'B' and (resid 129 through 152 )B129 - 152
16X-RAY DIFFRACTION16chain 'B' and (resid 153 through 199 )B153 - 199
17X-RAY DIFFRACTION17chain 'B' and (resid 200 through 225 )B200 - 225
18X-RAY DIFFRACTION18chain 'B' and (resid 226 through 246 )B226 - 246
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 16 )C2 - 16
20X-RAY DIFFRACTION20chain 'C' and (resid 17 through 40 )C17 - 40
21X-RAY DIFFRACTION21chain 'C' and (resid 41 through 54 )C41 - 54
22X-RAY DIFFRACTION22chain 'C' and (resid 55 through 67 )C55 - 67
23X-RAY DIFFRACTION23chain 'C' and (resid 68 through 82 )C68 - 82
24X-RAY DIFFRACTION24chain 'C' and (resid 83 through 128 )C83 - 128
25X-RAY DIFFRACTION25chain 'C' and (resid 129 through 152 )C129 - 152
26X-RAY DIFFRACTION26chain 'C' and (resid 153 through 173 )C153 - 173
27X-RAY DIFFRACTION27chain 'C' and (resid 174 through 185 )C174 - 185
28X-RAY DIFFRACTION28chain 'C' and (resid 186 through 199 )C186 - 199
29X-RAY DIFFRACTION29chain 'C' and (resid 200 through 225 )C200 - 225
30X-RAY DIFFRACTION30chain 'C' and (resid 226 through 246 )C226 - 246
31X-RAY DIFFRACTION31chain 'D' and (resid 2 through 16 )D2 - 16
32X-RAY DIFFRACTION32chain 'D' and (resid 17 through 54 )D17 - 54
33X-RAY DIFFRACTION33chain 'D' and (resid 55 through 82 )D55 - 82
34X-RAY DIFFRACTION34chain 'D' and (resid 83 through 152 )D83 - 152
35X-RAY DIFFRACTION35chain 'D' and (resid 153 through 199 )D153 - 199
36X-RAY DIFFRACTION36chain 'D' and (resid 200 through 225 )D200 - 225
37X-RAY DIFFRACTION37chain 'D' and (resid 226 through 246 )D226 - 246

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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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