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- PDB-4o94: Crystal structure of a trap periplasmic solute binding protein fr... -

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Basic information

Entry
Database: PDB / ID: 4o94
TitleCrystal structure of a trap periplasmic solute binding protein from Rhodopseudomonas palustris HaA2 (RPB_3329), Target EFI-510223, with bound succinate
ComponentsTRAP dicarboxylate transporter DctP subunit
KeywordsTRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function
TRAP transporter solute receptor, DctP family / Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
SUCCINIC ACID / TRAP dicarboxylate transporter DctP subunit
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionJan 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRAP dicarboxylate transporter DctP subunit
B: TRAP dicarboxylate transporter DctP subunit
C: TRAP dicarboxylate transporter DctP subunit
D: TRAP dicarboxylate transporter DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,71323
Polymers150,7094
Non-polymers1,00419
Water17,439968
1
A: TRAP dicarboxylate transporter DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8664
Polymers37,6771
Non-polymers1893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAP dicarboxylate transporter DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9737
Polymers37,6771
Non-polymers2956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TRAP dicarboxylate transporter DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9737
Polymers37,6771
Non-polymers2956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TRAP dicarboxylate transporter DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9025
Polymers37,6771
Non-polymers2244
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.469, 112.845, 136.294
Angle α, β, γ (deg.)90.00, 95.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TRAP dicarboxylate transporter DctP subunit


Mass: 37677.223 Da / Num. of mol.: 4 / Fragment: UNP residues 23-332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic)
Strain: HaA2 / Gene: RPB_3329 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2IUT5
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 968 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 4
Details: Protein (30.3 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM Succinate); Reservoir (1 M Lithium Chloride 0.1 M tri-Sodium Citrate pH 4, 20 %(w/v) PEG 6000); Cryoprotection (80% of 50% Peg3350, ...Details: Protein (30.3 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM Succinate); Reservoir (1 M Lithium Chloride 0.1 M tri-Sodium Citrate pH 4, 20 %(w/v) PEG 6000); Cryoprotection (80% of 50% Peg3350, 20% Reservoir), sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 26, 2013 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→135.57 Å / Num. all: 90352 / Num. obs: 90352 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 18.23 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 10.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.114.30.611.151688118900.6186.5
2.11-2.244.60.4541.555008118500.45491.6
2.24-2.395.10.34258496115810.3494.8
2.39-2.585.50.2652.561798111380.26597.8
2.58-2.836.20.1953.564091103850.19599.6
2.83-3.166.70.1345.26348094850.13499.8
3.16-3.657.10.0927.75929183720.092100
3.65-4.477.20.0699.95093670760.069100
4.47-6.327.40.06210.74054955090.062100
6.32-135.577.10.05212.52185730660.05299.6

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
PHENIXAUOTSOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→45.19 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.8643 / SU ML: 0.22 / σ(F): 0 / σ(I): 0 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 4544 5.03 %RANDOM
Rwork0.1631 ---
all0.1657 90284 --
obs0.1657 90284 95.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.3 Å2 / Biso mean: 22.849 Å2 / Biso min: 0.54 Å2
Refinement stepCycle: LAST / Resolution: 2→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9567 0 47 968 10582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139813
X-RAY DIFFRACTIONf_angle_d1.31613249
X-RAY DIFFRACTIONf_chiral_restr0.0761442
X-RAY DIFFRACTIONf_plane_restr0.0061731
X-RAY DIFFRACTIONf_dihedral_angle_d14.6113611
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 (%)
2-2.02270.3161270.20952524265184
2.0227-2.04650.22931440.19442512265687
2.0465-2.07150.28351510.1882557270887
2.0715-2.09770.26881400.18932649278988
2.0977-2.12530.24641330.18762654278788
2.1253-2.15440.28681400.18242669280991
2.1544-2.18520.27141410.18482748288992
2.1852-2.21780.22181310.17032780291191
2.2178-2.25250.2681240.16382768289294
2.2525-2.28940.23971750.16512752292794
2.2894-2.32890.21431660.15392842300893
2.3289-2.37120.25211490.14862821297097
2.3712-2.41680.20881790.15382860303997
2.4168-2.46610.22111520.15712879303197
2.4661-2.51980.22641560.15632939309599
2.5198-2.57840.22661590.15732945310498
2.5784-2.64290.23051630.15752917308099
2.6429-2.71430.23231480.16093012316099
2.7143-2.79420.22861480.171829423090100
2.7942-2.88430.21291890.17329773166100
2.8843-2.98740.24221490.169629543103100
2.9874-3.1070.23591570.175330363193100
3.107-3.24840.24511870.17229093096100
3.2484-3.41960.21391530.176729903143100
3.4196-3.63370.21951530.16329903143100
3.6337-3.91410.17141590.147430033162100
3.9141-4.30780.15141390.131930103149100
4.3078-4.93040.14271530.130229953148100
4.9304-6.20930.1791290.156330553184100
6.2093-45.20150.19211500.18573051320199
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)
10.04280.04170.0340.02880.03240.04110.059-0.00260.07430.0222-0.04390.0484-0.0627-0.0515-0.01250.09310.01460.02170.05190.00520.05918.955610.23515.0674
20.10190.0224-0.02110.26-0.06780.1599-0.00290.005-0.046-0.0437-0.0340.02020.01360.0093-0.03930.0712-0.0016-0.00540.0730.02190.064916.5639-2.68683.501
30.21620.09560.14890.26120.16370.1479-0.1046-0.09240.0168-0.0231-0.07160.0836-0.0822-0.0073-0.13790.13580.04240.01210.07160.07090.13918.754911.1564.4565
40.0156-0.00360.01030.00890.0009-0.0001-0.0470.0931-0.0645-0.05340.02630.01180.0420.07-0.00050.1666-0.05910.01170.1637-0.01820.116921.2367-6.4535-13.2519
50.005-0.0024-00.0042-0.00340.00040.01850.03560.04110.0007-0.06310.00420.028-0.0533-0.00010.2019-0.0068-0.03980.22320.01070.17534.8294-4.9424-14.977
60.0278-0.03390.03360.0691-0.01160.04410.06940.0027-0.0054-0.07350.03690.03630.08290.00080.1380.10060.004-0.05760.0666-0.0427-0.01689.2261-6.00549.6998
70.04250.05060.05550.11340.09990.1836-0.0534-0.07130.0459-0.0653-0.06390.0564-0.0405-0.0395-0.13050.00960.0178-0.00080.0736-0.01720.03595.24146.640563.5112
80.05570.00780.04180.01210.0050.03190.0044-0.08780.01930.0131-0.02460.03580.0109-0.1282-0.0230.00070.01160.00740.0821-0.04250.1046-1.55165.722160.565
90.00060.0002-0.0040.0265-0.00120.00470.00640.03370.00370.05240.0073-0.0131-0.0153-0.10910.00020.0409-0.0041-0.00090.0922-0.01880.055322.85584.521179.5458
100.01970.0071-0.01550.0157-0.01640.0253-0.0336-0.01820.07620.02670.025-0.0111-0.0870.0574-0.01770.0735-0.0006-0.01660.0691-0.00930.067522.298110.867668.7632
110.01730.03690.00130.0463-0.00750.00890.0091-0.05550.00290.040200.03010.0193-0.04060.00190.040.0135-0.00360.0628-0.00620.039514.58740.723764.2758
120.0111-0.00230.00930.01770.02340.0576-0.07220.0516-0.0562-0.0263-0.0060.04370.0905-0.0631-0.01260.1186-0.0268-0.02440.08250.00330.08625.7514-9.710661.1554
130.0055-0.0084-0.00060.00690.00430.0013-0.0326-0.0474-0.06440.05550.02450.0057-0.0303-0.0354-00.13810.03670.00320.1017-0.00150.06217.73562.716384.6334
140.0007-0.0032-0.00130.0106-0.00080.0002-0.0377-0.05280.0675-0.0155-0.0219-0.01190.0032-0.11680.00010.09450.016-00.2227-0.05310.15841.11813.659676.7508
150.01590.0003-0.0110.0235-0.00530.0087-0.03180.04810.03830.09480.0040.007-0.00360.0385-0.00050.0876-0.0114-0.00080.0603-0.02080.078415.3481-15.178640.1781
160.02630.00330.01690.0059-0.00030.0084-0.02330.04210.0257-0.0407-0.00530.0371-0.0378-0.0002-0.00730.0599-0.0117-0.00290.0614-0.01510.053217.3658-19.565824.6938
170.0026-0.0025-0.00310.00660.00380.0038-0.05440.0115-0.0424-0.01140.0277-0.0329-0.0048-0.0218-00.0748-0.0023-0.00320.0846-0.00270.109621.2862-38.016428.3006
180.0067-0.0111-0.00430.08860.06430.04730.04230.0548-0.0926-0.01360.0529-0.1608-0.0428-0.00370.01440.08690.0131-0.00370.1015-0.0080.100225.9757-25.117527.556
190.00350.00090.0030.01470.00740.0115-0.0306-0.00110.01650.04010.0388-0.02830.05630.022-00.0519-0.0051-0.00870.0624-0.00220.11591.4752-44.145627.0754
200.0154-0.00460.00540.0127-0.00590.0232-0.01920.10120.0058-0.03420.03860.0392-0.0046-0.01890.0484-0.1208-0.1773-0.0858-0.1468-0.10120.00532.0962-32.735321.7304
210.0515-0.04430.03090.04810.00880.03130.0221-0.05480.00790.0791-0.02340.03830.0270.02360.01480.0516-0.01610.01090.0624-0.00790.08679.5038-29.362932.1351
220.1063-0.0491-0.03390.15610.05830.0482-0.0501-0.08540.07870.14610.1159-0.12060.10460.03070.06220.0909-0.0329-0.03070.08210.02670.071618.5867-26.970542.8186
230.0130.0052-0.00110.0043-0.00160.00360.00090.0208-0.0647-0.00960.07990.0757-0.0063-0.02160.00050.12260.01510.01530.0902-0.02430.15285.9138-49.067428.4056
240.0031-0.00410.00150.02120.00640.0047-0.0830.0471-0.0587-0.06550.0017-0.16250.0213-0.00830.00040.09380.00010.00530.134-0.02230.150623.5217-40.704618.737
250.0020.00330.01210.0052-0.02610.06780.0858-0.0477-0.01140.1116-0.00650.03350.0626-0.12460.03290.0968-0.08020.0471-0.05950.1198-0.012617.965-38.1444108.2214
260.23930.0339-0.05710.0396-0.00970.0242-0.06050.1166-0.05970.00730.10560.1053-0.0357-0.08150.0080.08190.02450.0020.06820.02470.042417.4904-25.160394.0248
270.0377-0.01030.01060.0234-0.04640.116-0.0530.04060.15910.0630.09270.0312-0.0879-0.05620.01960.04590.0313-0.01530.07790.03370.105420.6551-20.891695.2481
280.00440.0008-0.0021-0.00010.00230.00380.01650.03860.0044-0.0362-0.0185-0.05930.0308-0.0362-00.09240.01990.01590.10330.01980.151932.9628-18.994588.3174
290.03030.01050.00430.0632-0.01610.08160.0164-0.0279-0.09490.1109-0.0034-0.1603-0.0195-0.05740.00060.05840.0279-0.02370.04290.00930.091229.4676-25.229799.2495
300.0766-0.00810.0560.08150.00130.0577-0.0766-0.0071-0.06050.20060.05410.0765-0.0753-0.1802-0.00340.1929-0.00870.04180.1367-0.01460.084915.8294-26.0878110.2873
310.07440.0543-0.08450.04-0.06070.09980.07360.00530.03810.06620.0654-0.023-0.04390.01840.01130.2540.012-0.03350.0597-0.01780.13333.4628-4.967298.6995
320.0019-0.0024-0.01050.00590.00110.0149-0.07650.01160.04710.03750.10240.1068-0.10590.0484-0.00040.09950.02180.00220.10740.02040.080517.4824-11.856186.523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 55 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 249 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 285 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 286 through 316 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 317 through 333 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 75 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 76 through 122 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 123 through 147 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 148 through 163 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 164 through 201 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 202 through 249 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 250 through 285 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 286 through 306 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 307 through 328 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 25 through 75 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 76 through 101 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 102 through 122 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 123 through 147 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 148 through 163 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 164 through 201 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 202 through 249 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 250 through 285 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 286 through 306 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 307 through 329 )C0
25X-RAY DIFFRACTION25chain 'D' and (resid 25 through 75 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 76 through 122 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 123 through 163 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 164 through 183 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 184 through 249 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 250 through 285 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 286 through 303 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 304 through 329 )D0

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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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