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- PDB-4xjy: Periplasmic repressor protein YfiR -

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Basic information

Entry
Database: PDB / ID: 4xjy
TitlePeriplasmic repressor protein YfiR
ComponentsYfiR
KeywordsSIGNALING PROTEIN / Inhibitor / Periplasm / Signal Transduction
Function / homologyYfiR/HmsC-like / YfiR/HmsC-like / periplasmic space / L(+)-TARTARIC ACID / Negative regulator YfiR
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKauer, S. / Schirmer, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A-138414 Switzerland
CitationJournal: To Be Published
Title: Periplasmic repressor protein YfiR at 1.8 Angstroms resolution
Authors: Kauer, S. / Schirmer, T.
History
DepositionJan 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations
Category: atom_site / diffrn_radiation_wavelength ...atom_site / diffrn_radiation_wavelength / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: YfiR
B: YfiR
C: YfiR
D: YfiR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2278
Polymers73,4504
Non-polymers7774
Water5,513306
1
A: YfiR
B: YfiR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2014
Polymers36,7252
Non-polymers4762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: YfiR
D: YfiR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0254
Polymers36,7252
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.691, 68.073, 71.989
Angle α, β, γ (deg.)90.000, 111.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid
31chain C and segid
41chain D and segid

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segidA0
211chain B and segidB0
311chain C and segidC0
411chain D and segidD0
Detailsbiological unit is the same as asym.

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Components

#1: Protein
YfiR


Mass: 18362.498 Da / Num. of mol.: 4 / Fragment: UNP residues 36-190
Source method: isolated from a genetically manipulated source
Details: C-terminal his-tag fusion / Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: yfiR, PA1121 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I4L4
#2: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.8 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris-HCl pH 8.0, 0.5 % Polyethylene glycol monoethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.799→47.756 Å / Num. all: 54499 / Num. obs: 54499 / % possible obs: 93.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.09 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.091 / Rsym value: 0.064 / Net I/av σ(I): 7.455 / Net I/σ(I): 16.8 / Num. measured all: 346155
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.940.1742447661450.1220.175.172.8
1.9-2.014.90.1742.83564372280.1030.1746.790.3
2.01-2.155.80.1642.24257573360.0860.1648.897.3
2.15-2.326.70.1432.54593568860.070.14311.797.9
2.32-2.557.30.116.14614763420.0520.1115.498.2
2.55-2.857.40.0897.34307958060.0430.08918.998.5
2.85-3.297.40.0649.53800751250.0320.06425.198.9
3.29-4.027.40.04811.73205443420.0240.04833.899.1
4.02-5.697.30.03415.82503534080.020.0343999.4
5.69-47.75670.029181320418810.0240.02938.498.2

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→47.756 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.84 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 4952 4.69 %
Rwork0.1733 100549 -
obs0.1753 54446 92.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.8 Å2 / Biso mean: 27.8379 Å2 / Biso min: 8.55 Å2
Refinement stepCycle: final / Resolution: 1.8→47.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 48 306 4944
Biso mean--32.15 30.53 -
Num. residues----595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114810
X-RAY DIFFRACTIONf_angle_d1.2256532
X-RAY DIFFRACTIONf_chiral_restr0.065753
X-RAY DIFFRACTIONf_plane_restr0.007864
X-RAY DIFFRACTIONf_dihedral_angle_d11.7951807
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2588X-RAY DIFFRACTION8.561TORSIONAL
12B2588X-RAY DIFFRACTION8.561TORSIONAL
13C2588X-RAY DIFFRACTION8.561TORSIONAL
14D2588X-RAY DIFFRACTION8.561TORSIONAL
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 (%)
1.8-1.82050.2816880.21441984207256
1.8205-1.84190.27891360.20982432256866
1.8419-1.86440.22421200.20492649276974
1.8644-1.8880.2571450.20182802294777
1.888-1.91280.22081420.20413012315483
1.9128-1.9390.21191500.20133135328585
1.939-1.96670.2291630.19923100326388
1.9667-1.99610.21551490.20113335348490
1.9961-2.02730.23331710.1963369354094
2.0273-2.06050.22561850.19423492367795
2.0605-2.0960.2551690.18583471364097
2.096-2.13410.19781760.17073496367297
2.1341-2.17520.22281580.16783583374198
2.1752-2.21960.19261880.183539372798
2.2196-2.26780.27891790.1863534371397
2.2678-2.32060.21281760.17143577375399
2.3206-2.37860.23371560.1743564372098
2.3786-2.44290.21491750.16643533370898
2.4429-2.51480.25631760.17993578375498
2.5148-2.5960.20721680.18053570373899
2.596-2.68880.20751900.18453605379599
2.6888-2.79640.22831760.1763549372599
2.7964-2.92370.2191820.18473552373499
2.9237-3.07780.22821790.18733594377398
3.0778-3.27060.21111690.18023569373899
3.2706-3.5230.23151730.16473596376999
3.523-3.87740.18181810.15323608378999
3.8774-4.43810.18061760.1393577375399
4.4381-5.59020.17171880.15543587377599
5.5902-47.7730.22251680.17313557372598
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)
10.6274-0.10730.19862.2745-0.26470.63210.4952-0.57090.1181-0.0323-0.3953-0.6365-0.06130.03680.15190.0957-0.0789-0.17720.2632-0.00550.00876.088236.720239.4162
20.55840.16720.01330.1862-0.28920.4850.072-0.12790.05040.033-0.06570.018-0.01880.0111-0.07650.14170.00140.0250.09030.02120.162871.881442.261430.5456
31.49430.37620.06390.64250.4420.24340.0584-0.02490.0290.109-0.0841-0.00840.0208-0.06920.04690.14340.00490.0360.11710.01170.163568.616342.707828.3449
40.3466-0.2713-0.11130.23190.12570.0983-0.0880.2545-0.3557-0.0926-0.01810.01860.0601-0.0802-0.15690.1583-0.03150.02940.1818-0.05330.152266.060833.856720.7867
50.1098-0.27610.09370.83280.45851.8711-0.17950.2494-0.5278-0.117-0.1494-0.05920.0105-0.1583-0.68480.22740.01420.13320.1616-0.04710.410671.425227.092927.5864
61.4859-0.0548-0.29170.1742-0.16540.6296-0.2086-0.4869-0.48610.0455-0.0457-0.08540.33020.2842-0.08860.29740.08710.08260.16340.11760.311675.593726.77538.9422
73.1694-0.578-0.00810.4281-0.21370.41150.04120.6959-1.1307-0.0626-0.15790.45310.2728-0.0432-0.0180.2380.04120.08790.07320.05860.380577.398427.988623.3621
80.0502-0.050.02820.0908-0.09140.1709-0.1564-0.06580.2097-0.0312-0.0612-0.0337-0.28950.271-0.00670.23710.04710.05740.23640.01410.259185.634335.919727.5161
90.15280.0827-0.05280.33740.13250.18060.18630.21860.28530.0283-0.0148-0.0652-0.4705-0.2822-0.09360.17140.03760.04730.15630.02550.25848.160542.594738.0919
100.5955-0.5040.18480.78720.32450.4460.081-0.1080.2943-0.0012-0.1078-0.1208-0.03890.101-0.22180.1384-0.03080.01860.151-0.03340.171952.204136.958349.0124
116.49252.25810.44871.7325-0.59920.66060.27390.51290.5742-0.196-0.1901-0.2733-0.312-0.150.02750.2839-0.06050.03960.1711-0.13170.267248.368845.750952.8079
120.3523-0.43990.10240.8311-0.26980.96270.3281-0.41420.2830.1309-0.2644-0.41710.10980.2869-0.0410.1467-0.0485-0.0230.2097-0.00230.199560.273131.903650.39
130.48530.3458-0.18560.1477-0.11920.37150.0016-0.1164-0.1191-0.0451-0.003-0.15660.08260.1897-0.00980.1567-0.0044-0.00850.1465-0.0080.14955.047724.634246.709
141.2587-0.02230.86040.8323-0.02950.8326-0.0213-0.1638-0.1940.15970.0742-0.00480.3084-0.13960.0450.1488-0.02410.02180.1303-0.00550.168747.36727.087943.7024
150.38650.15690.46950.19850.34020.7267-0.12120.77220.1837-0.02130.32860.0923-0.1933-0.12210.33660.2339-0.0866-0.01320.24560.10110.175944.723436.728932.5791
160.10930.0588-0.06670.1360.14070.18230.01520.2041-0.04440.04130.01270.25530.02040.0167-0.00340.1597-0.014-0.01440.14180.00440.168540.116926.384243.0347
170.01890.0142-0.02040.0108-0.017-0.00020.1329-0.03140.3740.3289-0.31690.5022-0.0759-0.3911-0.00050.1914-0.01280.02640.175-0.0410.179638.102830.259952.9556
180.08360.25620.16890.65610.46270.47670.37370.724-0.3466-0.3726-0.66660.2412-0.0792-0.2053-0.04480.22620.1346-0.0360.4476-0.00310.219433.907134.711541.3271
190.44490.0670.08221.28390.06950.48790.20750.1156-0.2427-0.2536-0.32010.1613-0.2855-0.4624-0.79760.22910.0259-0.07070.2502-0.01660.10219.985552.857347.1505
200.4471-0.04620.33260.1809-0.28660.4752-0.0925-0.0409-0.0130.06460.02-0.0004-0.0148-0.0809-0.15570.1031-0.001-0.01890.1147-0.01160.083917.021246.430354.1241
210.63980.3787-0.35570.6597-0.11350.9323-0.0537-0.1508-0.0718-0.07420.01750.00570.0016-0.1332-0.07520.12020.0069-0.00740.15040.00180.104617.906645.831857.9231
221.08310.4088-1.22290.7736-0.78971.62940.0997-0.2454-0.02050.4640.1021-0.2391-0.97650.64180.18480.2619-0.0725-0.09220.3181-0.04230.14423.500456.31767.4625
230.2719-0.11120.2610.68040.1060.4060.1203-0.2672-0.0774-0.17940.1087-0.1988-0.13080.18060.25580.0421-0.018-0.0360.1777-0.01620.122825.11551.345757.0853
240.90640.86110.03231.1288-0.010.85680.1175-0.01630.4566-0.0393-0.1203-0.312-0.23390.1730.4040.2518-0.05340.03090.20070.0010.289919.644661.636356.0808
250.0288-0.02820.00430.0752-0.00360.11880.1310.46250.4794-0.27080.0749-0.1045-0.3084-0.05050.00950.29050.04220.01960.19050.06070.233610.63862.234148.1198
260.8916-0.35040.55990.67770.44051.34140.20850.05980.6519-0.20520.0432-0.3203-0.75860.2680.26880.2033-0.0572-0.02340.20.01760.190425.95860.814451.8212
270.50120.5376-0.09491.10260.55772.41830.27240.136-0.007-0.61490.2588-0.4524-0.89760.37410.95180.404-0.00860.03890.13580.03780.162926.744354.932144.1975
281.66661.5018-0.38671.5352-0.30620.7483-0.1824-0.0703-0.7231-0.2369-0.2694-0.75380.61310.599-0.45240.3816-0.00560.12090.32770.02920.208820.647549.671136.9883
290.8049-0.3369-0.26470.4130.17160.2532-0.5121-0.4032-0.82320.25580.19170.23140.31940.1633-0.03130.20190.02730.02940.17050.03710.19441.524445.785973.6527
300.45820.1697-0.1710.4667-0.24670.6845-0.13950.1724-0.2103-0.11430.01810.0420.2498-0.076-0.05110.1171-0.0415-0.00090.171-0.03010.1661-7.265651.223565.9555
312.43571.5041-1.56831.1582-0.69991.5538-0.14540.1183-0.4669-0.1489-0.1846-0.38820.1804-0.0756-0.5850.1868-0.0493-0.01890.2194-0.06810.1492-8.532450.325462.3634
320.24230.0378-0.05060.62970.24090.3291-0.02220.1191-0.0846-0.32380.0224-0.1494-0.1142-0.1032-0.01580.1517-0.0214-0.02740.17780.00170.1379-4.263463.424263.9109
330.1854-0.0740.1340.8509-0.41731.7595-0.019-0.11190.15220.07670.13260.0701-0.0176-0.13210.1530.13620.0127-0.00280.1382-0.020.1805-3.967561.299772.3709
340.50690.32110.00260.38280.06020.1633-0.0876-0.27250.03470.24770.1902-0.04820.04340.23570.17830.16190.0629-0.02440.1813-0.0150.1332-1.314357.931978.8705
350.35740.53630.16930.66820.20250.2567-0.0767-0.159-0.12720.2173-0.08120.17170.09820.0222-00.25110.01720.05970.20740.03820.1717-9.200954.700580.5473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 58 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 84 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 119 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 139 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 151 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 160 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 161 through 171 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 172 through 194 )A0
9X-RAY DIFFRACTION9chain 'B' and (resid 38 through 58 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 84 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 85 through 93 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 94 through 105 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 106 through 130 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 131 through 151 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 152 through 160 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 161 through 171 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 172 through 177 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 178 through 185 )B0
19X-RAY DIFFRACTION19chain 'C' and (resid 39 through 58 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 59 through 84 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 85 through 119 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 120 through 130 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 131 through 139 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 140 through 151 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 152 through 160 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 161 through 171 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 172 through 183 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 184 through 198 )C0
29X-RAY DIFFRACTION29chain 'D' and (resid 38 through 58 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 59 through 84 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 85 through 105 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 106 through 130 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 131 through 151 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 152 through 171 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 172 through 185 )D0

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