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- PDB-6clu: Staphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208... -

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Basic information

Entry
Database: PDB / ID: 6clu
TitleStaphylococcus aureus Dihydropteroate Synthase (saDHPS) F17L E208K double mutant structure
ComponentsDihydropteroate synthase
KeywordsANTIMICROBIAL PROTEIN / antibiotic resistance mutations / sulfonamide resistance
Function / homology
Function and homology information


dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / response to antibiotic / metal ion binding
Similarity search - Function
Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel ...Dihydropteroate synthase signature 1. / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Dihydropteroate synthase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsGajewski, S. / Griffith, E.C. / Wu, Y. / White, S.W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI070721-08 United States
St. Jude Children's Research Hospital (ALSAC) United States
Department of Energy (DOE, United States)W-31-109-Eng-38 United States
CitationJournal: Front Microbiol / Year: 2018
Title: The Structural and Functional Basis for Recurring Sulfa Drug Resistance Mutations inStaphylococcus aureusDihydropteroate Synthase.
Authors: Griffith, E.C. / Wallace, M.J. / Wu, Y. / Kumar, G. / Gajewski, S. / Jackson, P. / Phelps, G.A. / Zheng, Z. / Rock, C.O. / Lee, R.E. / White, S.W.
History
DepositionMar 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Dihydropteroate synthase
B: Dihydropteroate synthase
C: Dihydropteroate synthase
D: Dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)129,6284
Polymers129,6284
Non-polymers00
Water3,549197
1
A: Dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)32,4071
Polymers32,4071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)32,4071
Polymers32,4071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)32,4071
Polymers32,4071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)32,4071
Polymers32,4071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Dihydropteroate synthase
B: Dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)64,8142
Polymers64,8142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-18 kcal/mol
Surface area19280 Å2
MethodPISA
6
C: Dihydropteroate synthase
D: Dihydropteroate synthase


Theoretical massNumber of molelcules
Total (without water)64,8142
Polymers64,8142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-20 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.636, 76.636, 176.226
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Dihydropteroate synthase / / DHPS / Dihydropteroate pyrophosphorylase


Mass: 32406.936 Da / Num. of mol.: 4 / Mutation: F17L, E208K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: folP, dpsA / Production host: Escherichia coli (E. coli) / References: UniProt: O05701, dihydropteroate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium Nitrate, and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97943 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.32
ReflectionResolution: 1.95→46.622 Å / Num. obs: 684630 / % possible obs: 99.9 % / Redundancy: 9.2 % / Net I/σ(I): 9.7
Reflection shellResolution: 1.95→1.99 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.622 Å / Cross valid method: THROUGHOUT / σ(F): 48.42 / Phase error: 30.43
RfactorNum. reflection% reflection
Rfree0.2036 2005 2.72 %
Rwork0.1819 --
obs0.1893 73613 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.61 Å2 / Biso mean: 32.2363 Å2 / Biso min: 18.27 Å2
Refinement stepCycle: final / Resolution: 1.95→46.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7039 0 0 197 7236
Biso mean---32.33 -
Num. residues----946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017142
X-RAY DIFFRACTIONf_angle_d0.3719690
X-RAY DIFFRACTIONf_chiral_restr0.041182
X-RAY DIFFRACTIONf_plane_restr0.0031245
X-RAY DIFFRACTIONf_dihedral_angle_d13.8834330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9505-1.99930.4371430.39285041518496
1.9993-2.05330.36151410.32575069521097
2.0533-2.11370.31191470.29045114526197
2.1137-2.18180.27191450.26895091523697
2.1818-2.25970.28571440.24065130527497
2.2597-2.350.25371420.22245085522797
2.35-2.45680.23191440.21625106525097
2.4568-2.58610.23091410.20775096523797
2.5861-2.74780.21291430.19595099524297
2.7478-2.95940.21091480.18125135528397
2.9594-3.25610.17761400.16425080522097
3.2561-3.72480.17131330.15665160529397
3.7248-4.68340.16781440.14085120526497
4.6834-20.40780.1881500.16435156530697
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)
11.72330.82340.24351.7630.12311.3190.16340.38460.30660.1077-0.1396-0.43590.31760.4127-0.08850.26320.0530.01220.32910.00090.37990.2239119.40017.9285
21.17510.27760.0870.0714-0.10861.6611-0.06080.07690.2779-0.06050.0625-0.16260.07990.09250.0650.22960.03380.04840.30640.02040.370590.2005123.42083.9821
30.29520.2626-0.26521.08461.35024.3997-0.4454-0.08630.1356-0.05-0.0557-0.4769-0.19580.29320.05420.2630.03540.02290.38240.03440.618592.2094134.44139.396
41.1863-0.1484-0.57461.1557-0.21151.33690.06710.04430.3566-0.0462-0.0599-0.2095-0.068-0.0711-0.01740.20010.0470.03190.24860.02320.356180.2767133.672110.448
51.37450.111-0.33741.6274-0.37961.54040.09940.0829-0.0860.0756-0.0282-0.04760.1235-0.0139-0.06620.23280.02880.01310.2196-0.00620.294473.2735123.282620.6815
61.0088-0.6767-0.16624.3755-1.54431.1257-0.098-0.01260.12870.03020.2239-0.0509-0.1395-0.2731-0.03820.16910.04060.01130.31790.0090.254766.2669125.463118.5231
71.25510.3106-0.96361.25590.36231.0686-0.087-0.0006-0.16340.06590.0706-0.01560.0852-0.00160.00130.1790.01560.01070.2068-0.01340.270275.4965113.866915.3862
81.68090.00710.08981.510.02860.89580.0354-0.0497-0.1325-0.1387-0.0065-0.14060.0702-0.0825-0.02280.19840.03650.02280.2547-0.02320.291679.7892109.3728.0123
93.99260.90641.50221.83140.32351.61080.12780.0684-0.0722-0.2632-0.01580.18220.0792-0.0709-0.03170.30230.029-0.01090.25750.00190.304575.6388107.8843-2.3288
101.10730.5001-0.21650.41640.07810.1805-0.1351-0.0139-0.1229-0.05550.0919-0.02010.14060.17230.0550.20110.0258-0.00020.28410.00520.360286.160183.5375-0.5719
111.4640.29970.35760.9842-0.16081.11270.06290.1298-0.0442-0.2285-0.0705-0.37780.22120.08680.07190.29690.0510.06290.2917-0.00410.423183.188273.8502-4.894
121.9124-0.5808-0.08121.62960.01321.1978-0.00130.1562-0.107-0.3635-0.1037-0.06860.0931-0.03430.07690.3105-0.00090.03310.2983-0.02090.344173.631473.038-6.2938
131.70560.566-0.31692.3814-0.00431.0649-0.159-0.14350.0319-0.07850.1062-0.04740.0729-0.01990.08190.16410.0129-0.01080.2240.00150.271764.440983.1234-3.8602
141.45550.76980.89961.47910.79090.80340.1760.12170.0196-0.061-0.13040.1407-0.1485-0.1604-0.02120.19940.0162-0.01520.2477-0.01320.268972.855693.24880.943
151.4642-1.2738-1.72061.28421.67272.65760.00540.0038-0.39770.085-0.15380.1444-0.060.00420.07880.2150.0004-0.02420.24910.00970.312276.188498.833411.8471
161.3329-0.38280.23962.215-0.94581.33650.0766-0.1135-0.20260.36350.00160.1223-0.00740.03630.01720.3201-0.06220.01930.18760.01950.380999.0521111.4116-25.9188
170.64360.11930.22631.25120.08690.9718-0.0888-0.1269-0.4095-0.0652-0.1498-0.05110.01020.04260.04940.3524-0.01040.02330.21240.05920.4956101.8841105.1905-24.4436
181.3540.94041.371.39431.53232.87220.1621-0.2833-0.21120.3604-0.1436-0.01970.301-0.0215-0.00580.41540.0354-0.01880.27560.08530.5142113.6606107.3938-16.8527
191.86810.1067-0.02262.4970.73431.5521-0.2429-0.0189-0.2440.09260.16590.1427-0.02360.35180.13240.2911-0.01190.00910.20650.08170.354112.2672113.1693-23.0211
200.68570.0112-0.42731.67340.42311.4438-0.0213-0.0479-0.25560.10490.0532-0.28710.05110.0476-0.01940.2949-0.0443-0.01830.17890.0360.3544112.8786122.5908-21.3512
211.4861-0.65470.1441.87710.16290.4970.1655-0.04120.0312-0.12730.01190.0373-0.0423-0.0866-0.06390.2644-0.044-0.06010.19420.05440.289104.2176126.4927-21.7599
224.1534-0.7035-0.96261.27930.02520.77450.0933-0.3290.04420.1335-0.0417-0.1561-0.10080.1996-0.04550.3311-0.0539-0.03860.15870.0220.2416104.7312134.5206-23.1009
231.36850.0777-0.14291.39880.10710.7986-0.1777-0.214-0.3892-0.001-0.1932-0.0409-0.05010.18750.06540.3243-0.0334-0.0430.18770.02520.2646101.605125.9535-23.9409
241.34240.4492-0.73861.1213-0.06722.10670.12480.04230.00280.0946-0.06760.2443-0.1814-0.38650.01750.3014-0.05850.01140.2508-0.00730.334690.438131.8482-22.496
251.49930.1973-0.09540.64950.01290.77480.2585-0.2394-0.0080.4335-0.21640.2517-0.09220.0026-0.00410.3547-0.06650.0360.26080.01220.358391.0858121.4011-21.3572
261.48890.09110.10212.219-0.16770.7535-0.0679-0.0561-0.18670.30520.04280.0067-0.0649-0.06540.06540.3058-0.04140.01750.21590.00310.299488.352117.2691-24.9778
271.8542-0.72210.85111.9569-1.07773.2708-0.11630.2836-0.0534-0.0833-0.0274-0.4867-0.0382-0.30210.06070.2192-0.0270.00860.253-0.0260.367187.1117116.337-37.2421
280.85770.32830.26681.2526-0.15020.5797-0.03370.0782-0.42520.23830.03330.27120.3387-0.0661-0.03140.3427-0.02910.06130.2015-0.00230.530665.2755104.7935-32.8086
292.72511.94860.24112.69940.39590.9955-0.15-0.2871-0.26510.4679-0.1386-0.02510.43050.03080.08160.5264-0.0250.14550.26530.07230.503362.9129103.0712-23.2674
301.36390.7052-0.130.63820.38210.7496-0.1075-0.0904-0.78130.2312-0.01350.51650.3194-0.06290.12970.3476-0.05980.1660.27930.03790.725754.8989105.406-32.7593
311.5987-0.15570.57531.1693-0.26052.2716-0.0856-0.22140.01730.238-0.06130.5560.0287-0.3029-0.00560.3142-0.05010.1550.2017-0.00620.728252.1815111.1271-32.8624
321.5667-0.5219-0.63961.55080.10261.13410.06230.1279-0.18790.0739-0.02620.5910.0621-0.10980.00620.2373-0.01390.02760.2737-0.03880.50156.0092117.7555-43.9315
331.1936-0.4305-0.27111.1209-0.22020.51120.16880.0093-0.12390.0636-0.1150.3702-0.0995-0.0963-0.0630.2557-0.01960.02980.2324-0.03710.369961.6836123.6526-44.8076
341.0675-1.1535-0.8142.68241.34631.7098-0.0073-0.0658-0.0532-0.0419-0.05330.06-0.12470.15940.03970.2354-0.00410.01310.25420.00070.287274.6589122.9604-45.7013
351.5912-1.33320.16882.3635-0.09140.77160.0252-0.16930.0714-0.01840.1334-0.12840.078-0.0775-0.18130.2173-0.02820.0240.1828-0.00290.382868.9686118.1404-37.9509
360.9121-0.4664-0.5873.0925-0.87870.89180.05790.1574-0.2787-0.5151-0.0838-0.78610.33910.0717-0.0540.38250.01340.05290.2824-0.04570.446682.0505106.8204-42.6287
371.48030.2858-0.02041.83550.05551.323-0.0757-0.126-0.0886-0.08890.07350.05320.0220.0357-0.02110.2434-0.0240.01680.216-0.00670.298875.9232114.5755-34.0822
381.51571.47530.45224.58670.99840.70860.0767-0.15420.21470.38490.01790.2032-0.06610.0736-0.11210.294-0.04540.05190.2149-0.00850.302977.7453122.6389-23.9845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )A2 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 59 )A26 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 74 )A60 - 74
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 121 )A75 - 121
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 138 )A122 - 138
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 157 )A139 - 157
7X-RAY DIFFRACTION7chain 'A' and (resid 158 through 216 )A158 - 216
8X-RAY DIFFRACTION8chain 'A' and (resid 217 through 242 )A217 - 242
9X-RAY DIFFRACTION9chain 'A' and (resid 243 through 260 )A243 - 260
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 59 )B2 - 59
11X-RAY DIFFRACTION11chain 'B' and (resid 60 through 87 )B60 - 87
12X-RAY DIFFRACTION12chain 'B' and (resid 88 through 111 )B88 - 111
13X-RAY DIFFRACTION13chain 'B' and (resid 112 through 190 )B112 - 190
14X-RAY DIFFRACTION14chain 'B' and (resid 191 through 242 )B191 - 242
15X-RAY DIFFRACTION15chain 'B' and (resid 243 through 264 )B243 - 264
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 25 )C2 - 25
17X-RAY DIFFRACTION17chain 'C' and (resid 26 through 59 )C26 - 59
18X-RAY DIFFRACTION18chain 'C' and (resid 60 through 74 )C60 - 74
19X-RAY DIFFRACTION19chain 'C' and (resid 75 through 97 )C75 - 97
20X-RAY DIFFRACTION20chain 'C' and (resid 98 through 121 )C98 - 121
21X-RAY DIFFRACTION21chain 'C' and (resid 122 through 138 )C122 - 138
22X-RAY DIFFRACTION22chain 'C' and (resid 139 through 157 )C139 - 157
23X-RAY DIFFRACTION23chain 'C' and (resid 158 through 175 )C158 - 175
24X-RAY DIFFRACTION24chain 'C' and (resid 176 through 192 )C176 - 192
25X-RAY DIFFRACTION25chain 'C' and (resid 193 through 215 )C193 - 215
26X-RAY DIFFRACTION26chain 'C' and (resid 216 through 242 )C216 - 242
27X-RAY DIFFRACTION27chain 'C' and (resid 243 through 262 )C243 - 262
28X-RAY DIFFRACTION28chain 'D' and (resid 2 through 25 )D2 - 25
29X-RAY DIFFRACTION29chain 'D' and (resid 26 through 39 )D26 - 39
30X-RAY DIFFRACTION30chain 'D' and (resid 40 through 74 )D40 - 74
31X-RAY DIFFRACTION31chain 'D' and (resid 75 through 97 )D75 - 97
32X-RAY DIFFRACTION32chain 'D' and (resid 98 through 138 )D98 - 138
33X-RAY DIFFRACTION33chain 'D' and (resid 139 through 175 )D139 - 175
34X-RAY DIFFRACTION34chain 'D' and (resid 176 through 192 )D176 - 192
35X-RAY DIFFRACTION35chain 'D' and (resid 193 through 203 )D193 - 203
36X-RAY DIFFRACTION36chain 'D' and (resid 204 through 215 )D204 - 215
37X-RAY DIFFRACTION37chain 'D' and (resid 216 through 242 )D216 - 242
38X-RAY DIFFRACTION38chain 'D' and (resid 243 through 263 )D243 - 263

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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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