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- PDB-9mi2: Crystal structure of Purine nucleoside phosphorylase from Trichom... -

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Basic information

Entry
Database: PDB / ID: 9mi2
TitleCrystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (C2 form)
ComponentsPurine nucleoside phosphorylase, putative
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Purine nucleoside phosphorylase / Trichomonas vaginalis
Function / homology
Function and homology information


uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase activity / cytosol
Similarity search - Function
Purine nucleoside phosphorylase DeoD-type / Nucleoside phosphorylase, conserved site / Purine and other phosphorylases family 1 signature. / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily
Similarity search - Domain/homology
Purine nucleoside phosphorylase, putative
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Purine nucleoside phosphorylase from Trichomonas vaginalis (C2 form)
Authors: Mian, M.R. / Lovell, S. / Liu, L. / Battaile, K.P.
History
DepositionDec 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Purine nucleoside phosphorylase, putative
B: Purine nucleoside phosphorylase, putative
C: Purine nucleoside phosphorylase, putative
D: Purine nucleoside phosphorylase, putative
E: Purine nucleoside phosphorylase, putative
F: Purine nucleoside phosphorylase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,50513
Polymers159,8616
Non-polymers6457
Water15,403855
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21240 Å2
ΔGint-164 kcal/mol
Surface area46210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.269, 50.364, 175.485
Angle α, β, γ (deg.)90.00, 98.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Purine nucleoside phosphorylase, putative


Mass: 26643.428 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_454490 / Plasmid: TrvaA.01033.d.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2EU62
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Berkeley C8: 20% (w/v) PEG 3350, 100 mM magnesium chloride, 100 mM NaCl, TrvaA.01033.d.B1.PW39308 at 17.4 mg/mL. plate 14462 well C8 drop 1, Puck: PSL1411. Cryo: 20% Glycerol + 80% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 26, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.8→48.25 Å / Num. obs: 136883 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.05 / Rrim(I) all: 0.113 / Χ2: 1 / Net I/σ(I): 9 / Num. measured all: 705878
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.872 / Num. measured all: 35407 / Num. unique obs: 6707 / CC1/2: 0.74 / Rpim(I) all: 0.416 / Rrim(I) all: 0.968 / Χ2: 1.06 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIXdev_5533refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.25 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 6864 5.02 %
Rwork0.1637 --
obs0.1654 136822 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10701 0 42 855 11598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911034
X-RAY DIFFRACTIONf_angle_d0.99914998
X-RAY DIFFRACTIONf_dihedral_angle_d13.5124011
X-RAY DIFFRACTIONf_chiral_restr0.0581749
X-RAY DIFFRACTIONf_plane_restr0.0121937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.27432140.2394262X-RAY DIFFRACTION100
1.82-1.840.26452230.24584290X-RAY DIFFRACTION100
1.84-1.860.24432250.22544384X-RAY DIFFRACTION100
1.86-1.890.25752220.2144266X-RAY DIFFRACTION100
1.89-1.910.26232300.20724259X-RAY DIFFRACTION100
1.91-1.940.27122110.20894409X-RAY DIFFRACTION100
1.94-1.970.30022250.21024246X-RAY DIFFRACTION100
1.97-20.26892300.21084323X-RAY DIFFRACTION100
2-2.030.21982350.18554314X-RAY DIFFRACTION100
2.03-2.060.22922360.16874255X-RAY DIFFRACTION100
2.06-2.10.20492150.16094350X-RAY DIFFRACTION100
2.1-2.130.22042390.16114251X-RAY DIFFRACTION100
2.13-2.180.18422310.15754394X-RAY DIFFRACTION100
2.18-2.220.22622360.15654266X-RAY DIFFRACTION100
2.22-2.270.20552340.1594321X-RAY DIFFRACTION100
2.27-2.320.21192200.15854289X-RAY DIFFRACTION100
2.32-2.380.18682100.15444369X-RAY DIFFRACTION100
2.38-2.440.19522350.14994316X-RAY DIFFRACTION100
2.44-2.510.20092040.15974375X-RAY DIFFRACTION100
2.51-2.60.20682570.16424269X-RAY DIFFRACTION100
2.6-2.690.18842100.15564363X-RAY DIFFRACTION100
2.69-2.80.20412030.16074381X-RAY DIFFRACTION100
2.8-2.920.20032410.16624327X-RAY DIFFRACTION100
2.92-3.080.1752170.17084333X-RAY DIFFRACTION100
3.08-3.270.21712470.16914339X-RAY DIFFRACTION100
3.27-3.520.18942520.16064336X-RAY DIFFRACTION100
3.52-3.880.18782470.15294369X-RAY DIFFRACTION99
3.88-4.440.14172480.13194321X-RAY DIFFRACTION99
4.44-5.590.16562530.13624422X-RAY DIFFRACTION100
5.59-48.250.2032140.18344559X-RAY DIFFRACTION99
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)
10.73180.58080.95332.57481.83671.78930.1083-0.23570.54970.2819-0.1660.0254-0.56650.29790.07020.4541-0.1468-0.0150.2637-0.03160.2847-26.211341.469771.8362
24.75161.0364-0.74411.6897-0.34584.32620.0902-0.3467-0.17410.2872-0.1773-0.2663-0.12560.75740.08740.2867-0.0492-0.04280.3208-0.01730.1975-19.656326.071673.7581
30.76050.2853-0.40611.01030.27890.57460.125-0.28820.13080.1407-0.0617-0.1215-0.25090.388-0.01970.3049-0.1364-0.02340.321-0.03540.2217-23.031933.075870.6989
41.42790.0759-0.43645.72281.25682.54420.0409-0.1031-0.0848-0.1098-0.1494-0.07750.04440.43440.08530.1898-0.0354-0.03280.28780.04330.1937-20.82320.871260.9945
51.9765-0.7090.52371.3174-0.45882.30890.0703-0.0480.00920.0624-0.0666-0.0079-0.02560.09930.00360.2017-0.0478-0.01730.1512-0.01730.1978-30.434226.592950.729
68.8335-6.51566.55126.9194-4.21538.77020.02730.32290.3248-0.0643-0.3063-0.873-0.09580.8270.24850.176-0.0739-0.00670.4730.02520.3033-9.501124.849655.7587
71.7804-0.2647-0.55611.348-0.16542.1061-0.11880.1241-0.06790.03220.039-0.01340.29480.16310.06160.22450.0235-0.02580.1274-0.00070.173-26.936314.749857.8639
81.8932-0.098-0.03950.91730.3352.71740.0311-0.1105-0.2260.1276-0.0438-0.07730.24770.26960.01180.1877-0.0203-0.01570.17020.02240.1863-25.629317.964656.9385
93.90352.3979-0.69668.7715-1.66984.43940.0188-0.379-0.06420.47910.1067-0.38160.0530.5993-0.08610.2786-0.0364-0.08440.48770.02440.2572-12.648119.931267.8329
103.3393-0.2336-1.9520.0825-0.06913.2467-0.0084-0.3305-0.10650.1177-0.03150.0049-0.04640.32150.03020.2732-0.0342-0.01950.13830.01730.2087-41.81621.129783.2393
110.61290.0212-0.33550.0645-0.07121.36950.04450.0402-0.00680.0843-0.03040.0162-0.15-0.0764-0.00650.2673-0.02050.01520.10820.00460.2188-48.653724.369267.8052
123.6658-3.0934-1.77083.33580.64933.5251-0.01790.1119-0.35160.2164-0.15740.33830.5144-0.42560.05970.2567-0.04070.02850.1597-0.02360.2142-63.014227.282776.8783
131.7651-0.0636-0.89610.31620.42122.47860.1060.10610.16280.10590.00010.026-0.4004-0.0216-0.14190.3080.01410.00550.06720.01570.2262-48.827136.028363.5594
140.4646-0.3586-0.40211.09990.76520.62310.12570.04910.10580.1504-0.0481-0.0077-0.3061-0.0622-0.01280.3627-0.00780.03310.1354-00.2574-50.689932.655765.2208
154.12914.0426-0.48798.4816-1.62341.79170.0971-0.1480.18260.1811-0.0422-0.237-0.29470.1691-0.02910.3114-0.02230.04040.1446-0.03920.2032-52.97633.806882.014
163.0866-0.9880.51611.1116-0.24911.72360.1150.4416-0.1905-0.0814-0.1366-0.17670.29090.80690.01080.23660.09570.00870.4527-0.01140.2373-12.762516.389422.7339
172.2462-0.0106-0.1591.0318-0.12421.94590.01680.06030.02870.1102-0.054-0.17280.02170.47440.02070.14770.0054-0.01150.2240.01950.1425-18.764422.427332.084
181.34740.1191-0.42580.6557-0.20971.84380.0334-0.0310.0803-0.01-0.0389-0.1139-0.14420.34090.00080.1888-0.0522-0.02130.17580.0060.2053-23.844828.967940.5381
192.1690.6454-0.51632.5365-0.43572.77860.05870.05330.2823-0.0134-0.0606-0.0215-0.23620.3085-0.00540.1812-0.0249-0.02430.2380.01070.2397-20.952928.406635.783
203.7278-2.44390.82963.2271-3.4215.48060.09890.31420.3873-0.1742-0.234-0.5163-0.2290.68960.16240.279-0.071-0.01040.54190.04840.3753-7.931830.634830.732
212.2423-0.25210.63251.3411-0.19634.20760.03060.30180.1177-0.0921-0.0864-0.0306-0.13970.29340.05240.22130.01010.01020.24420.03530.2064-30.365926.72547.6936
221.17940.0155-0.15230.76270.13232.60370.08110.11620.0575-0.0811-0.09140.1270.0644-0.112-0.0120.17970.0161-0.01740.1502-0.00170.1692-38.5622.49316.0096
230.6055-0.2057-0.44691.54961.73245.85760.05530.0664-0.0923-0.0246-0.14510.0514-0.036-0.51650.10250.1655-0.0028-0.0260.201-0.01260.2041-48.451623.038221.3895
240.7447-0.3478-0.24550.3087-0.51482.5887-0.0042-0.0307-0.1813-0.0184-0.08450.05660.4885-0.25860.06940.2898-0.0605-0.00510.1661-0.03440.246-44.072511.224925.1134
250.9153-0.4567-0.09474.13480.14741.9340.10010.0949-0.10240.0996-0.180.01550.3493-0.1340.05020.2262-0.0161-0.02290.1764-0.02180.2009-42.290517.165519.3908
263.1429-1.90771.04362.3537-2.97165.24870.1690.222-0.0095-0.4413-0.2201-0.2650.42660.04090.03490.24340.0109-0.02770.238-0.05260.2138-40.908213.70835.4997
272.4666-0.54320.86551.0803-0.13210.30790.05440.26750.269-0.0394-0.0450.3755-0.2675-0.2324-0.04260.37970.25920.06970.87020.16260.4888-79.954237.760245.1424
280.2601-0.09830.03260.560.09150.0265-0.0695-0.1414-0.09150.10190.11010.39590.0187-0.53610.01270.2362-0.04070.00620.93950.08210.4102-83.120222.514851.2693
290.0046-0.0092-0.00010.34670.01410.0026-0.07520.32450.20570.08990.19730.2769-0.2778-0.9209-0.05850.25640.13920.04480.89470.07950.4331-79.687829.857349.1956
301.4312-0.8755-0.62291.47140.68051.7114-0.13740.0932-0.15810.06010.12590.11360.215-0.71210.01030.2164-0.07240.02580.44630.00480.293-70.896319.166656.9879
312.79660.414-1.38951.5218-0.42874.10840.04640.21030.0557-0.00740.05070.0219-0.13-0.4105-0.11020.20050.03440.00030.2070.00050.1682-58.029226.058353.288
328.88955.5949-3.71086.3201-3.33845.55250.2009-0.0320.29350.4689-0.05310.4299-0.2718-0.6465-0.12010.2340.04810.05560.43890.0130.2725-72.493924.286668.7313
331.48550.2284-0.20371.4329-0.37571.5492-0.01960.1323-0.247-0.05130.0940.07910.3241-0.4410.01320.243-0.09240.0060.2721-0.01220.2676-62.194313.039454.391
341.4449-0.1822-0.152.9486-0.26531.5311-0.05130.2342-0.2179-0.0687-0.01790.40830.2745-0.69440.03010.2752-0.05710.0520.3462-0.00770.2687-67.748419.208354.9603
352.73420.77590.02037.11320.75712.5556-0.07750.181-0.3326-0.01050.19930.39950.1636-0.8899-0.07210.2516-0.08030.04750.7760.0210.403-80.729117.362560.7931
360.56070.3494-0.09740.33030.19980.6195-0.0690.3307-0.0922-0.11490.010.33640.1366-0.6918-0.41490.1404-0.2521-0.05181.24960.03670.4031-78.213416.210328.9579
371.09110.04570.04530.3340.01230.592-0.03250.3827-0.0746-0.10510.08210.20790.1581-1.0068-0.0190.217-0.1341-0.03660.7933-0.00980.2903-67.24519.826428.7173
381.3066-0.37541.05721.2306-0.71622.30540.01770.54090.1373-0.08450.11840.1511-0.1615-0.63640.0650.17590.0009-0.01060.6180.0720.2728-62.218129.143723.3366
391.93590.06560.18520.2729-0.41181.8773-0.05610.26620.2051-0.05660.09760.3299-0.1452-0.782-0.00940.24270.0345-0.01630.48520.00580.2408-60.935929.354227.8257
401.73670.12320.36474.6724-0.22491.7945-0.20720.06150.28380.11890.52070.4245-0.1049-0.9267-0.2440.3085-0.0052-0.01841.14360.04620.4575-74.680528.295717.523
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 103 )
5X-RAY DIFFRACTION5chain 'A' and (resid 104 through 131 )
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 144 )
7X-RAY DIFFRACTION7chain 'A' and (resid 145 through 166 )
8X-RAY DIFFRACTION8chain 'A' and (resid 167 through 214 )
9X-RAY DIFFRACTION9chain 'A' and (resid 215 through 236 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 55 )
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 131 )
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 145 )
13X-RAY DIFFRACTION13chain 'B' and (resid 146 through 166 )
14X-RAY DIFFRACTION14chain 'B' and (resid 167 through 214 )
15X-RAY DIFFRACTION15chain 'B' and (resid 215 through 236 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 55 )
17X-RAY DIFFRACTION17chain 'C' and (resid 56 through 103 )
18X-RAY DIFFRACTION18chain 'C' and (resid 104 through 182 )
19X-RAY DIFFRACTION19chain 'C' and (resid 183 through 214 )
20X-RAY DIFFRACTION20chain 'C' and (resid 215 through 236 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 55 )
22X-RAY DIFFRACTION22chain 'D' and (resid 56 through 103 )
23X-RAY DIFFRACTION23chain 'D' and (resid 104 through 144 )
24X-RAY DIFFRACTION24chain 'D' and (resid 145 through 182 )
25X-RAY DIFFRACTION25chain 'D' and (resid 183 through 214 )
26X-RAY DIFFRACTION26chain 'D' and (resid 215 through 236 )
27X-RAY DIFFRACTION27chain 'E' and (resid 1 through 15 )
28X-RAY DIFFRACTION28chain 'E' and (resid 16 through 33 )
29X-RAY DIFFRACTION29chain 'E' and (resid 34 through 79 )
30X-RAY DIFFRACTION30chain 'E' and (resid 80 through 103 )
31X-RAY DIFFRACTION31chain 'E' and (resid 104 through 131 )
32X-RAY DIFFRACTION32chain 'E' and (resid 132 through 144 )
33X-RAY DIFFRACTION33chain 'E' and (resid 145 through 182 )
34X-RAY DIFFRACTION34chain 'E' and (resid 183 through 214 )
35X-RAY DIFFRACTION35chain 'E' and (resid 215 through 236 )
36X-RAY DIFFRACTION36chain 'F' and (resid 1 through 33 )
37X-RAY DIFFRACTION37chain 'F' and (resid 34 through 131 )
38X-RAY DIFFRACTION38chain 'F' and (resid 132 through 166 )
39X-RAY DIFFRACTION39chain 'F' and (resid 167 through 214 )
40X-RAY DIFFRACTION40chain 'F' and (resid 215 through 236 )

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  • 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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