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- PDB-7t7u: Light Harvesting complex phycocyanin PC 630, from the cryptophyte... -

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Basic information

Entry
Database: PDB / ID: 7t7u
TitleLight Harvesting complex phycocyanin PC 630, from the cryptophyte Chroomonas sp. M1627
Components
  • (Phycoerythrin alpha subunit ...) x 2
  • Phycoerythrin beta subunit
KeywordsPHOTOSYNTHESIS / PHOTOSYNTHESIS light harvesting globin fold
Function / homology
Function and homology information


phycobilisome / plastid / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Phycoerythrin alpha chain / Phycoerythrin-like alpha chain superfamily / Phycoerythrin, alpha/beta chain / Globular protein, non-globular alpha/beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Globin-like superfamily
Similarity search - Domain/homology
DiCys-(15,16)-Dihydrobiliverdin / PHYCOCYANOBILIN / mesobiliverdin IX(alpha) / Phycoerythrin alpha subunit S1 / Phycoerythrin beta subunit / Phycoerythrin alpha subunit L1
Similarity search - Component
Biological speciesChroomonas sp. M1627 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMichie, K.A. / Harrop, S.J. / Rathbone, H.W. / Wilk, K.E. / Curmi, P.M.G.
Funding support United States, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)ARC LIEF LE190100165
Australian Research Council (ARC)DP180103964
Other governmentFA2386-17-1-4101 United States
Citation
Journal: Protein Sci. / Year: 2023
Title: Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins.
Authors: Michie, K.A. / Harrop, S.J. / Rathbone, H.W. / Wilk, K.E. / Teng, C.Y. / Hoef-Emden, K. / Hiller, R.G. / Green, B.R. / Curmi, P.M.G.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycoerythrin alpha subunit L1
B: Phycoerythrin beta subunit
C: Phycoerythrin alpha subunit S1
D: Phycoerythrin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,42813
Polymers52,6304
Non-polymers4,7989
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19410 Å2
ΔGint-139 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.294, 93.411, 132.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-420-

HOH

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Components

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Phycoerythrin alpha subunit ... , 2 types, 2 molecules AC

#1: Protein Phycoerythrin alpha subunit L1


Mass: 8877.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas sp. M1627 (eukaryote) / References: UniProt: A0A067XP78
#3: Protein Phycoerythrin alpha subunit S1 / Phycoerythrin alpha subunit S2


Mass: 7599.737 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas sp. M1627 (eukaryote) / References: UniProt: A0A067XP68

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Protein , 1 types, 2 molecules BD

#2: Protein Phycoerythrin beta subunit


Mass: 18076.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas sp. M1627 (eukaryote) / References: UniProt: A0A067XP72

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Non-polymers , 5 types, 461 molecules

#4: Chemical ChemComp-M1V / mesobiliverdin IX(alpha)


Mass: 586.678 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H38N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-AX9 / DiCys-(15,16)-Dihydrobiliverdin / 15,16-DIHYDROBILIVERDIN (double Cys bound form) / 3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(Z)-(3-ethyl-4-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{[(2R)-4-ethyl-3-methyl-5-oxo-2,5-dihydro-1H-pyrrol-2-yl]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 3,350 20-28%, HEPES 100 mM pH7.5 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.8→39.5 Å / Num. obs: 51263 / % possible obs: 98.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 16.01 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.076 / Rrim(I) all: 0.123 / Net I/σ(I): 8.5
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.047 / Num. unique obs: 7267 / Rpim(I) all: 0.333 / Rrim(I) all: 0.702

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALA3.3.16data scaling
PHASERphasing
MOSFLM2.0.6data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LMS
Resolution: 1.8→39.58 Å / SU ML: 0.1508 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.8743
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1849 2622 5.12 %
Rwork0.1579 48630 -
obs0.1593 51252 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 350 452 4347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01224108
X-RAY DIFFRACTIONf_angle_d1.26045607
X-RAY DIFFRACTIONf_chiral_restr0.0627612
X-RAY DIFFRACTIONf_plane_restr0.0096707
X-RAY DIFFRACTIONf_dihedral_angle_d15.9125680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.24841390.23622468X-RAY DIFFRACTION96.2
1.83-1.870.24771250.2272465X-RAY DIFFRACTION96.75
1.87-1.910.2381150.20572523X-RAY DIFFRACTION97.52
1.91-1.950.23341260.19012526X-RAY DIFFRACTION97.82
1.95-1.990.20851270.18522537X-RAY DIFFRACTION98.45
1.99-2.040.22271480.16992533X-RAY DIFFRACTION98.78
2.04-2.10.19011400.1652548X-RAY DIFFRACTION98.71
2.1-2.160.1981270.1532568X-RAY DIFFRACTION98.97
2.16-2.230.17931370.15432513X-RAY DIFFRACTION98.95
2.23-2.310.15731560.15222574X-RAY DIFFRACTION99.2
2.31-2.40.19461470.14632531X-RAY DIFFRACTION99.11
2.4-2.510.21191560.14642571X-RAY DIFFRACTION99.31
2.51-2.640.16161600.14322539X-RAY DIFFRACTION98.97
2.64-2.810.18371120.14332608X-RAY DIFFRACTION99.31
2.81-3.030.17481370.15262568X-RAY DIFFRACTION99.3
3.03-3.330.17151470.15282588X-RAY DIFFRACTION98.95
3.33-3.810.19081280.1392603X-RAY DIFFRACTION99.13
3.81-4.80.14461450.13182636X-RAY DIFFRACTION99.18
4.8-39.580.17941500.18042731X-RAY DIFFRACTION98.8
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)
10.802947361661-0.2141213448130.5840798692940.390325129616-0.08212968169221.053708639040.133707047139-0.07199109782420.0743342889752-0.0180093152916-0.104623052066-0.0378473560849-0.00384756860606-0.0125765672294-0.008106378898590.15904914719-0.0152359525435-0.003006575792240.102875667470.01818584558280.094444002351917.065833780932.9831682318150.22443469
21.19901892169-0.2629810019640.4178108531070.387939618561-0.09804645069980.441447670759-0.0285754968712-0.1900442307030.1807169814780.42393102217-0.05031643442570.13332909608-0.130784677346-0.2173461744320.08394256235970.231485429897-0.001947593060740.007948733315920.198030963653-0.007505242211490.14456398714529.295741515819.1009697092182.324452786
30.684605378239-0.255001872120.09019092454580.760917074576-0.06039944852740.614247621099-0.0228560679451-0.0569118341065-0.0005736678482080.07489930271830.003136405217310.070208875074-0.0773975599183-0.01587039231450.01985026371820.0891631161271-0.01548248037250.01183980531590.08703541123560.004407328458090.090068983996115.433618062128.1792563681166.450806858
40.43789195424-0.0935135994171-0.3389694472880.5041733317050.5621288700380.757676651873-0.1240817347210.28813503813-0.0325105746772-0.2130204297440.103105612962-0.1188432096870.05514390496350.04348988070420.1618045738170.2734636669810.0303395309990.1458769329360.3734938729570.09949487601640.27825950567939.674580963330.2665586701135.960614732
53.6801357642-0.704318381906-0.1586228507260.336671282455-0.004583994813580.571249861258-0.09041291082750.02093547431530.142344167193-0.152548143249-0.0456911942939-0.1543204235790.02165062700010.1049878889340.08867281617890.1610883797090.0323966011743-0.007640234783140.1546706092790.04632507626160.11784538969120.248650981531.4591831494138.724415257
62.510664762590.832924695637-0.8190160053381.53764911384-0.1309555014280.791158066966-0.06685197996150.03265448452340.353847216942-0.03081552301290.01643940636990.0532354279456-0.295797444223-0.2001053458380.003556478594860.2073161819770.00935556278766-0.06962963407580.1237939536530.0004282928094680.1300364746916.4229197376339.9063864186138.812716289
71.11568891489-0.03846567728330.3183335075440.2665649787810.090304411210.537598340796-0.05462118831480.1195527948030.148502164847-0.0932129484493-0.0624992775939-0.108435056168-0.07683889237160.1715821634820.1109814713520.205148819956-0.00410357401406-0.002777261277890.154040321230.05100825419050.11295122172212.833013239835.391762568132.425523937
80.466536455408-0.491811675848-0.3882362485560.9369793064870.4419074133731.40675577253-0.02805014582160.1442390066050.216147902521-0.204178194276-0.02202140505-0.112614545218-0.07668659290870.134681292880.01743994804450.103193924384-0.0239126643146-0.01215956890130.130499826720.05381451417060.1321351558132.845189602428.4069248019157.15528735
90.7850807586780.3699549088380.3390081787250.9257761021640.2460602054650.9260939123290.05014202078580.0679009598447-0.02223363858256.50541887701E-5-0.08604375855310.04147264819830.104772081690.06268203882130.0330780576840.1110416264410.00339721068864-0.01080936746420.1042016803370.009177828199950.10948709491526.235247863311.1337326902159.537837202
101.140371630120.852163899246-0.5522676626661.57979502461-0.9825879568215.318981155690.1211261472910.3187920687370.110754064645-0.09835395533330.2593315525260.06373330529730.103188213949-0.313079061133-0.2634720561870.1210278963030.04107748032260.02285208524770.2123811797640.04760913035320.19196866617940.81799112227.5584261864156.586304882
110.506379294045-0.4031890785470.3808494267940.652379732549-0.4844947821840.4024316508170.05954740894620.1696443606550.00775441822621-0.156112130475-0.131278438264-0.05202478826990.09907843728650.1817499291170.07617445384420.1334882847070.02148931601620.01938386840320.1391747911760.02970298928330.083169139561923.687933816722.5730519459142.856462377
120.3345939984420.0428839155126-0.1388647495970.518893126936-0.0513453585020.6919881401570.05144585200440.09201623350670.0315688613589-0.147149921512-0.126840111654-0.111347142189-0.009138275144370.205373100810.01561165084830.1716395798320.05671844807610.06387865229160.1703699504710.06610813971040.11518979517631.225128864925.0093541832143.131814359
130.631560414630.0622867769081-0.2291288265770.57605073421-0.2562250640620.310990319269-0.03855109730110.2023425978010.0690048630532-0.246313679301-0.0658061090535-0.07834489486620.1680203205990.1420116000870.07321855001830.2338248859650.06022610659570.0436018338710.2027975240920.04516823924030.11028131949527.071004499417.4027010226141.278932424
140.737232591131-0.2390248116230.2475427397080.726405847467-0.1035297646490.2695550441960.07198266586640.124180724817-0.121651359678-0.278806636656-0.0869908690588-0.04295879045430.1674215495920.1792897040780.05698346167430.398530889250.1380623923870.04361926956730.2158727101680.005925015665230.13793967450726.567034080413.0349938241135.780775942
150.732617420706-0.3244217669040.07249034397971.095273033270.01038313154340.514083251838-0.0433748858879-0.1205095852550.1181211875680.207189275617-0.0100939197037-0.0392245271644-0.06452799637250.060974497020.03463422706120.149542131116-0.0221516331955-0.03510960130820.134802262690.008100291955360.11428640385426.955507995131.2843574509172.594098807
160.3267950024750.05856191676070.01549317095590.4311400475630.1576983694951.0681777469-0.003649565054860.00747235718098-0.0575243257820.1301522966430.024709264667-0.1701321646540.2255186850210.387534401841-0.001047801036410.1529405369360.00880623606111-0.0244126423940.190783943410.04256243860170.1476773490641.165880640812.2178655683174.798371782
170.477390530666-0.7915486691470.1635897967273.26561051409-0.8761537920220.5042335825290.01303621915260.0354873460780.0365490070787-0.0769205210128-0.05144747508050.02634091680240.007637960496130.05624548308840.03319353292460.147270881703-0.0246875066165-0.0371252521930.1579563235660.004220127245490.15560146667632.954233002418.9043711215174.95745685
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 48 through 70 )CH48 - 7048 - 70
22chain 'D' and (resid 5 through 33 )DJ5 - 331 - 24
33chain 'D' and (resid 34 through 177 )DJ34 - 17725 - 168
44chain 'A' and (resid 1 through 6 )AA1 - 61 - 6
55chain 'A' and (resid 7 through 15 )AA7 - 157 - 15
66chain 'A' and (resid 16 through 25 )AA16 - 2516 - 25
77chain 'A' and (resid 26 through 46 )AA26 - 4626 - 46
88chain 'A' and (resid 47 through 61 )AA47 - 6147 - 61
99chain 'A' and (resid 62 through 76 )AA62 - 7662 - 76
1010chain 'A' and (resid 77 through 81 )AA77 - 8177 - 81
1111chain 'B' and (resid 16 through 75 )BC16 - 751 - 60
1212chain 'B' and (resid 76 through 99 )BC76 - 9961 - 84
1313chain 'B' and (resid 100 through 158 )BC100 - 15885 - 143
1414chain 'B' and (resid 159 through 177 )BC159 - 177144 - 162
1515chain 'C' and (resid 1 through 15 )CH1 - 151 - 15
1616chain 'C' and (resid 16 through 34 )CH16 - 3416 - 34
1717chain 'C' and (resid 35 through 47 )CH35 - 4735 - 47

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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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