[English] 日本語
Yorodumi
- PDB-4oa4: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oa4
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM SHEWANELLA LOIHICA PV-4 (Shew_1446), TARGET EFI-510273, WITH BOUND SUCCINATE
ComponentsTRAP dicarboxylate transporter, DctP subunit
KeywordsPROTEIN BINDING / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


organic substance transport / 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 / C4-dicarboxylate-binding periplasmic protein DctP
Similarity search - Component
Biological speciesShewanella loihica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 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 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)150,34717
Polymers149,5564
Non-polymers79113
Water36,8592046
1
A: TRAP dicarboxylate transporter, DctP subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6135
Polymers37,3891
Non-polymers2244
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)37,5784
Polymers37,3891
Non-polymers1893
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)37,5784
Polymers37,3891
Non-polymers1893
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)37,5784
Polymers37,3891
Non-polymers1893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.216, 117.950, 89.430
Angle α, β, γ (deg.)90.000, 93.000, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
TRAP dicarboxylate transporter, DctP subunit


Mass: 37388.996 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella loihica (bacteria) / Strain: PV-4 / Gene: Shew_1446 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3QCW5
#2: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2046 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (34.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM L-Malate); Reservoir (0.1 M Bis-Tris Propane pH 7, 2 M di-Ammonium Hydrogen Citrate); Cryoprotection (Reservoir with 20% Glycerol), ...Details: Protein (34.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM L-Malate); Reservoir (0.1 M Bis-Tris Propane pH 7, 2 M di-Ammonium Hydrogen Citrate); Cryoprotection (Reservoir with 20% Glycerol), VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
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 20, 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: 1.6→117.95 Å / Num. all: 217024 / Num. obs: 217024 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.79 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.50.5361.4112128317790.536100
1.69-1.793.60.3832107192299520.38399.6
1.79-1.913.60.2622.8101518280160.26299.3
1.91-2.073.70.1784.195469261380.17899.3
2.07-2.263.70.1345.287767240400.13499.4
2.26-2.533.60.1185.679634218700.11899.8
2.53-2.923.70.0966.671109193320.09699.8
2.92-3.583.80.076861819164200.076100
3.58-5.063.80.0629.548363126960.062100
5.06-25.2233.70.05311.32501267810.05396.1

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→25.223 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.8995 / SU ML: 0.15 / σ(F): 0 / σ(I): 0.811 / Phase error: 17.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 10898 5.02 %RANDOM
Rwork0.1538 ---
obs0.1552 216923 99.44 %-
all-216923 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.01 Å2 / Biso mean: 20.9141 Å2 / Biso min: 7.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9621 0 41 2046 11708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110003
X-RAY DIFFRACTIONf_angle_d1.20913546
X-RAY DIFFRACTIONf_chiral_restr0.0731491
X-RAY DIFFRACTIONf_plane_restr0.0061777
X-RAY DIFFRACTIONf_dihedral_angle_d14.0663740
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 (%)
1.6-1.61820.28253470.2668357182100
1.6182-1.63720.28283780.251169207298100
1.6372-1.65720.25493230.234769167239100
1.6572-1.67820.26013830.228868617244100
1.6782-1.70020.24453750.217768247199100
1.7002-1.72350.24723520.204968767228100
1.7235-1.74810.2243710.19986846721799
1.7481-1.77420.22833600.19226831719199
1.7742-1.80190.22953700.18716826719699
1.8019-1.83150.24133460.18586911725799
1.8315-1.8630.20194040.16896781718599
1.863-1.89690.20493890.16416791718099
1.8969-1.93340.19453720.15946779715199
1.9334-1.97280.19663510.15576851720299
1.9728-2.01570.18813670.15196818718599
2.0157-2.06260.18193660.1476861722799
2.0626-2.11410.1853660.14466833719999
2.1141-2.17130.17153540.14256865721999
2.1713-2.23510.16393710.1366853722499
2.2351-2.30720.193680.1468527220100
2.3072-2.38960.1723280.137868867214100
2.3896-2.48520.17463610.137969097270100
2.4852-2.59820.17173600.1468997259100
2.5982-2.7350.16983590.140768887247100
2.735-2.90620.17873640.14569147278100
2.9062-3.13020.17523540.14469107264100
3.1302-3.44450.15473670.145569477314100
3.4445-3.94130.15243850.133669117296100
3.9413-4.95940.13823450.12570087353100
4.9594-25.22620.18873620.16876823718597
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)
11.2965-0.3256-0.24490.73890.22880.56080.00140.01860.3242-0.069-0.01080.1172-0.1987-0.0721-0.01350.19190.002-0.02810.1035-0.00070.187171.129971.912565.2973
20.3299-0.0161-0.28411.2649-0.26470.401-0.0057-0.05850.01840.0076-0.03890.0381-0.0450.02510.03330.1155-0.0225-0.01120.1181-0.00570.094577.432857.075973.9938
31.51910.74150.04162.73760.20720.95970.0003-0.1504-0.02230.24630.0099-0.0352-0.07880.05630.00210.0992-0.00550.00130.12290.00650.084468.952855.198379.4355
40.8404-0.4692-0.2851.10830.28040.806-0.0819-0.012-0.12480.05150.010.01820.18270.06040.04560.135-0.00120.00530.11480.00860.107880.946744.123858.9953
50.56680.26190.08381.1234-0.48051.25-0.0046-0.06250.0032-0.0144-0.0609-0.13360.06130.18170.04960.0928-0.00280.00210.13050.02160.133889.329550.699263.2404
61.93010.08130.42050.8751-0.00560.8021-0.00520.1340.0452-0.14430.0002-0.0774-0.02520.0490.00920.1186-0.00630.00330.09840.00530.092682.714953.889153.9449
70.6563-0.00760.01750.91340.16270.361-0.029-0.07830.07270.1212-0.0114-0.00790.0087-0.02870.05170.1075-0.0201-0.02240.0906-0.00280.109774.10958.804269.5652
81.2192-0.6338-0.87381.60611.50762.40510.01120.04030.0765-0.0486-0.08710.1261-0.0725-0.24330.12270.10380.0005-0.02040.10730.00590.133964.869560.866462.6196
91.10160.03990.58991.3708-0.34651.6980.0136-0.0336-0.0468-0.09010.01290.02360.1108-0.0279-0.04970.1833-0.003-0.01330.12710.00070.158879.271737.622957.5762
101.5803-0.0447-0.10631.27470.11941.7578-0.0138-0.2078-0.15650.1225-0.0339-0.01480.20110.0574-0.00240.1176-0.0023-0.00210.14640.05770.123776.856441.677279.3169
110.81140.05820.3110.75850.11750.95460.0369-0.0918-0.16950.0347-0.0180.09870.1224-0.0953-0.02340.10640.01390.00530.12030.01330.161234.958934.357764.5987
120.56950.5250.3531.26820.05571.4598-0.08030.05620.1083-0.017-0.05280.1066-0.1278-0.13380.09820.12190.0441-0.02280.1230.01450.180537.07155.892258.7755
131.8088-1.2048-0.10893.00450.57631.29830.03070.07670.163-0.3362-0.04060.104-0.13350.01340.01610.12340.0351-0.01810.13460.01020.169630.414549.674552.7642
140.89740.30430.2970.57770.28180.4547-0.0016-0.10.1469-0.0192-0.06960.0664-0.0514-0.07960.0640.09820.03260.00180.1186-0.00630.139542.691654.103270.6993
151.03250.43710.77651.76381.60222.48470.0619-0.16570.0650.0877-0.1510.18750.0333-0.36060.10140.10350.00550.02020.2006-0.00730.184525.928143.869269.2627
161.0636-0.2272-0.08281.5711-0.61781.7035-0.0341-0.21530.38130.25960.02620.0504-0.316-0.2057-0.04520.18020.0587-0.00410.2117-0.07050.322137.527468.309176.9665
171.70590.17780.87390.90450.49771.3513-0.120.03660.3872-0.1226-0.0521-0.0135-0.352-0.06760.14060.20960.0552-0.04710.1730.05890.273736.180564.869755.2107
180.71710.26060.03590.7684-0.17511.0517-0.0292-0.10330.05150.11570.01810.0992-0.1309-0.04180.00770.14140.01340.01140.1360.02410.109353.350641.198391.4649
191.69310.00150.3391.49020.57730.760.07010.0568-0.02320.11870.00880.00820.08-0.0489-0.05510.14520.0155-0.01130.13880.03440.111660.80520.442987.195
200.74170.13290.23972.7588-0.78961.47440.00160.0187-0.02020.0703-0.0772-0.24940.08710.16820.06610.15270.0201-0.02790.15520.03270.149766.208626.286194.6999
210.50710.2914-0.08381.0725-0.02910.65530.02090.0397-0.04720.00420.00170.10750.1318-0.0651-0.01870.1319-0.0097-0.00480.15440.04230.126248.70221.673381.7223
222.26911.57580.90122.24570.82561.24210.0184-0.2938-0.13640.1959-0.06910.06670.0145-0.17350.04290.18850.01050.05360.17320.03780.122149.384530.277999.4903
231.48570.26310.08541.05030.04030.96760.041-0.0328-0.2520.11970.02970.10420.3068-0.017-0.04770.23840.0150.00110.14370.0430.166355.55959.684286.2878
240.56520.1379-0.37070.8446-0.11111.3197-0.0814-0.1121-0.14530.1910.0037-0.01970.18710.07930.0740.17140.02270.01640.13330.00580.130965.62398.155248.9325
250.71070.26870.0891.31120.25890.712-0.01640.0848-0.14430.0689-0.05880.21380.0488-0.06870.07580.093-0.00180.01540.0949-0.02180.14456.18898.380441.2362
261.381-0.1876-0.38851.3519-0.52370.71240.0040.03840.03290.0226-0.02780.0378-0.05040.00850.03210.12180.0082-0.00390.1252-0.02740.106453.69727.518241.2356
270.84890.4087-0.04333.48320.89111.1646-0.09670.0239-0.0280.0060.00480.3189-0.0442-0.11820.07230.10670.01250.01260.1191-0.0350.157149.308321.866549.3369
280.5566-0.20460.22970.6394-0.15320.63190.00610.08830.0338-0.0711-0.03330.0041-0.07110.02280.02810.1563-0.0058-0.0040.13760.00110.085264.990730.165430.9593
290.9585-0.08070.28540.79060.42131.82990.00870.0448-0.0048-0.0944-0.0129-0.10950.06990.10870.01310.1029-0.00980.01050.1063-0.00150.091673.620726.578734.9941
300.32160.117-0.12941.1811-0.17420.7008-0.0417-0.0287-0.04150.0167-0.02380.15870.0449-0.02980.05420.0964-0.00190.01150.0955-0.01590.11658.922419.50244.6193
311.76441.3631-0.72572.2734-0.86791.14610.0014-0.2242-0.00050.1766-0.0619-0.01080.01440.08310.03320.14380.01250.00110.1293-0.00610.091166.63420.216653.7971
323.2038-1.17290.5861.2368-0.22190.9662-0.07860.12380.1397-0.0994-0.0174-0.0301-0.17790.0850.13170.1824-0.0145-0.02580.1052-0.01280.083767.816441.937536.9971
331.39620.36140.21271.18430.57511.97350.09630.15360.16510.0001-0.12820.2599-0.0691-0.15620.06810.14670.0483-0.0120.1856-0.02530.17946.564334.876940.488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 82 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 122 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 150 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 151 through 170 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 171 through 207 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 229 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 230 through 256 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 257 through 292 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 293 through 313 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 314 through 336 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 32 through 98 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 99 through 122 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 123 through 150 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 151 through 256 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 257 through 292 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 293 through 310 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 311 through 336 )B0
18X-RAY DIFFRACTION18chain 'C' and (resid 32 through 98 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 99 through 122 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 123 through 150 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 151 through 256 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 257 through 292 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 293 through 336 )C0
24X-RAY DIFFRACTION24chain 'D' and (resid 33 through 82 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 83 through 98 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 99 through 122 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 123 through 150 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 151 through 207 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 208 through 229 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 230 through 256 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 257 through 292 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 293 through 313 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 314 through 335 )D0

+
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