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- PDB-4rj0: The crystal structure of Y333N mutant pyridoxal-dependent decarbo... -

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Basic information

Entry
Database: PDB / ID: 4rj0
TitleThe crystal structure of Y333N mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745
ComponentsPyridoxal-dependent decarboxylase
KeywordsLYASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / A/B/A FOLD / CYTOSOLIC
Function / homology
Function and homology information


sulfinoalanine decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Aspartate Aminotransferase, domain 1 - #170 / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Aspartate Aminotransferase, domain 1 - #170 / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Pyridoxal-dependent decarboxylase
Similarity search - Component
Biological speciesSphaerobacter thermophilus DSM 20745 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of Y333N mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745
Authors: Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Pyridoxal-dependent decarboxylase
A: Pyridoxal-dependent decarboxylase
C: Pyridoxal-dependent decarboxylase
D: Pyridoxal-dependent decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,8859
Polymers212,2664
Non-polymers6195
Water13,349741
1
B: Pyridoxal-dependent decarboxylase
A: Pyridoxal-dependent decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3174
Polymers106,1332
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13790 Å2
ΔGint-107 kcal/mol
Surface area29800 Å2
MethodPISA
2
C: Pyridoxal-dependent decarboxylase
D: Pyridoxal-dependent decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5685
Polymers106,1332
Non-polymers4353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-119 kcal/mol
Surface area29870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.984, 124.198, 129.942
Angle α, β, γ (deg.)90.00, 99.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyridoxal-dependent decarboxylase


Mass: 53066.422 Da / Num. of mol.: 4 / Mutation: Y333N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus DSM 20745 (bacteria)
Gene: Sthe_2364 / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D1C7D8, glutamate decarboxylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.04M KPO4, 16% PEG8k, 20% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2013 / Details: MIRRORS
RadiationMonochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 150109 / Num. obs: 144197 / % possible obs: 93.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 18.15 Å2 / Rsym value: 0.05 / Net I/σ(I): 8.1
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.593 / % possible all: 93

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Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RIT
Resolution: 1.95→32.558 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1927 7159 5.01 %
Rwork0.1677 --
obs0.1689 142776 91.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→32.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14318 0 39 741 15098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01714671
X-RAY DIFFRACTIONf_angle_d1.42519960
X-RAY DIFFRACTIONf_dihedral_angle_d15.075352
X-RAY DIFFRACTIONf_chiral_restr0.1232250
X-RAY DIFFRACTIONf_plane_restr0.0092619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.24372180.2144040X-RAY DIFFRACTION81
1.9722-1.99540.24122210.20184186X-RAY DIFFRACTION86
1.9954-2.01970.23052030.19954283X-RAY DIFFRACTION87
2.0197-2.04520.22752320.19854398X-RAY DIFFRACTION88
2.0452-2.07220.24312170.19874372X-RAY DIFFRACTION88
2.0722-2.10050.23082450.18694387X-RAY DIFFRACTION89
2.1005-2.13050.21522410.18144475X-RAY DIFFRACTION90
2.1305-2.16230.20452280.17684435X-RAY DIFFRACTION89
2.1623-2.19610.22572600.1774433X-RAY DIFFRACTION91
2.1961-2.23210.21432550.18164404X-RAY DIFFRACTION89
2.2321-2.27060.21972230.1844535X-RAY DIFFRACTION91
2.2706-2.31190.2362350.17644542X-RAY DIFFRACTION91
2.3119-2.35630.22672370.1764531X-RAY DIFFRACTION92
2.3563-2.40440.22632380.17254596X-RAY DIFFRACTION92
2.4044-2.45670.22132490.17784556X-RAY DIFFRACTION92
2.4567-2.51380.20032420.17364566X-RAY DIFFRACTION93
2.5138-2.57660.20822540.16774609X-RAY DIFFRACTION92
2.5766-2.64630.20332570.17394539X-RAY DIFFRACTION92
2.6463-2.72410.19922600.17054554X-RAY DIFFRACTION93
2.7241-2.8120.20532500.18054568X-RAY DIFFRACTION92
2.812-2.91240.20262390.17864592X-RAY DIFFRACTION92
2.9124-3.0290.17992400.1784612X-RAY DIFFRACTION92
3.029-3.16670.20432350.16894588X-RAY DIFFRACTION93
3.1667-3.33350.19122310.16924686X-RAY DIFFRACTION94
3.3335-3.54210.17212420.16634653X-RAY DIFFRACTION93
3.5421-3.81520.15952340.14944708X-RAY DIFFRACTION94
3.8152-4.19840.15912400.13954699X-RAY DIFFRACTION94
4.1984-4.80430.14232680.13684695X-RAY DIFFRACTION95
4.8043-6.04660.18642390.15964729X-RAY DIFFRACTION94
6.0466-32.56260.15882260.15254646X-RAY DIFFRACTION91
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)
11.8149-1.03880.13972.67240.2951.63550.14370.28940.0412-0.4607-0.1990.0576-0.2145-0.09570.03550.15280.01340.01380.16650.02870.0851-13.93824.57229.4545
21.3371-1.68160.47083.7221-0.08570.69320.12770.05210.3307-0.3252-0.0739-0.6755-0.08680.1122-0.06260.1346-0.03230.09620.20670.07450.22653.6421.894537.7121
30.6482-0.19120.21251.4227-0.29350.52350.01220.0445-0.0278-0.1687-0.0345-0.01860.04730.05970.0170.0688-0.00550.01240.1164-0.00460.0781-9.73119.236842.4744
41.2985-0.70780.07181.84550.12781.8603-0.0533-0.1123-0.03010.18190.0598-0.0025-0.04120.0006-0.0150.0646-0.01870.01250.0950.03820.1209-11.79442.684168.1097
50.9886-0.3687-0.27371.67990.5070.7467-0.0143-0.1015-0.08110.2582-0.0205-0.24150.05430.1510.03620.087-0.0054-0.03160.1340.040.1381-1.1866-4.422570.2652
60.86-0.0209-0.73881.2123-1.51813.1564-0.01720.0447-0.0827-0.0699-0.007-0.00680.14470.0440.02340.0488-0.00260.01180.0830.00460.1262-6.9554-6.446254.9798
70.45880.22810.57611.0092-0.34941.2031-0.028-0.0699-0.02390.16290.08640.3331-0.0689-0.36-0.02160.07170.01590.04240.18680.03390.2178-23.67175.674259.3318
82.5058-0.00360.18411.417-0.84181.36910.15490.0492-0.1937-0.2697-0.3424-0.45210.25820.4220.1348-0.01480.05430.11030.2360.08970.27610.6769-4.921348.3917
91.9331-0.2420.80451.153-0.3221.73110.04630.1266-0.0438-0.1597-0.2628-0.38880.13950.5280.16850.11190.03270.08040.28410.09050.314615.7122-1.317545.9128
104.4072-2.81570.03113.4631-0.01711.9640.16710.367-0.3177-0.4877-0.15580.07520.17570.0671-0.01950.1814-0.0060.00390.1574-0.03420.1182-8.47014.149528.5389
111.104-1.0994-0.08654.07630.92350.62420.06010.1533-0.2421-0.3092-0.08680.420.0953-0.10480.01750.1104-0.0241-0.03570.173-0.01780.1479-24.81810.310638.2328
120.1406-0.2181-0.35260.5222-0.02731.25660.0073-0.00840.10090.002-0.0102-0.1409-0.02040.11390.00390.0444-0.02530.00940.11560.0010.1367-3.515221.491653.3245
135.4295-4.05332.28643.8433-1.69872.9399-0.2144-0.5295-0.25270.41240.35710.16440.0418-0.1973-0.15950.1615-0.02640.02080.13610.00560.1213-13.463919.787975.1258
141.0634-0.40650.13571.8796-0.40510.3657-0.0441-0.16350.05280.30950.04730.1602-0.0022-0.0778-00.0952-0.00870.04040.1353-0.01380.1013-20.306429.163671.3826
150.8365-0.32540.64410.99731.09632.63660.00690.00450.06680.0015-0.0279-0.0632-0.0572-0.04280.02590.042-0.02360.00780.0810.00280.1106-14.594131.888856.1668
160.66840.3919-0.6230.89560.10661.2476-0.074-0.0951-0.02290.00560.0481-0.42280.05690.32810.02050.07230.0022-0.01270.18790.01430.2042.112819.62359.6957
172.8311-0.1785-0.55121.12680.27121.07810.049-0.06440.1627-0.0371-0.05140.2662-0.0995-0.2225-0.02240.04870.0106-0.01430.14110.00080.1304-32.444630.585549.4561
181.63970.0091-1.28891.0016-0.06911.91860.087-0.0571-0.0085-0.0999-0.08070.3016-0.1087-0.2301-0.01340.0513-0.0118-0.02130.164-0.00910.1975-37.08227.482647.3742
191.85181.276-0.73972.1297-1.23151.77170.196-0.33240.00960.5757-0.2744-0.2797-0.30890.37790.07220.4252-0.0293-0.11980.2743-0.01150.1994-10.365376.290526.6002
200.84741.6738-0.23044.2705-0.09970.3460.1874-0.15440.26290.6942-0.12610.3594-0.15960.0437-0.05840.44490.00830.0150.2177-0.02680.1493-29.544670.70729.047
211.40040.27640.82311.0233-0.1710.9411-0.03530.1534-0.0596-0.13220.024-0.0360.0470.14830.01660.2480.0298-0.00050.1106-0.00370.0988-21.830359.5023.8151
222.05451.7126-1.57473.0759-2.98995.026-0.06790.35580.0793-0.50190.33120.41290.145-0.3085-0.26020.43-0.0237-0.13710.18310.00590.2339-43.458760.8932-6.8218
230.6511-0.1466-0.47421.6232-0.51331.0437-0.05980.10.0039-0.23650.08360.36090.1351-0.2193-0.01790.2655-0.0263-0.08590.1270.00310.1927-43.999950.84111.0242
240.98390.53820.31492.317-0.08631.6051-0.01360.1331-0.0914-0.19340.0104-0.1050.17260.13860.01580.23580.0331-0.01290.1137-0.00670.1151-27.059555.07333.4111
252.24240.5835-0.24531.0061-0.12591.29430.0615-0.2587-0.02920.2672-0.0290.2352-0.0499-0.2462-0.02460.33230.0420.01520.17760.01440.1592-42.301250.494226.7615
260.66590.5368-0.06752.1753-0.59311.32120.2428-0.3014-0.22850.7145-0.278-0.3361-0.01510.15120.04890.40760.0198-0.10790.22460.01040.1892-14.749856.247128.7883
270.58170.6754-0.32545.682-2.21121.0636-0.04650.0281-0.2075-0.256-0.1038-0.55490.17780.17220.10560.22380.0397-0.01160.22670.00220.1971-6.979264.577210.5845
280.7074-0.12490.64521.2495-0.42731.61150.0575-0.10480.04810.11760.04620.1672-0.0544-0.0695-0.10980.26430.02070.01480.129-0.00980.1157-33.150476.571513.4368
295.36583.1257-1.32783.1905-1.47061.5838-0.12260.5059-0.2759-0.49730.23480.17640.1095-0.2927-0.13420.44830.0197-0.09430.19680.01360.1913-39.255176.0186-9.6742
300.99010.3058-0.10650.99310.29210.49290.07750.17480.082-0.3608-0.0280.12150.0134-0.0405-0.0470.37060.0299-0.04650.14020.02970.1314-31.146485.8301-8.3323
311.79270.31330.3471.6447-0.25780.8294-0.024-0.11720.13040.03760.03410.1492-0.1152-0.0501-0.01740.24580.02850.00390.1095-0.01730.0876-31.937681.48998.2776
321.732-0.0375-0.79441.1904-0.89581.8710.19760.19380.1095-0.167-0.1819-0.2327-0.04010.2189-0.02040.24670.02280.01690.1812-0.00660.153-6.49185.0021-1.35
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid -1 through 38 )
2X-RAY DIFFRACTION2chain 'B' and (resid 39 through 64 )
3X-RAY DIFFRACTION3chain 'B' and (resid 65 through 136 )
4X-RAY DIFFRACTION4chain 'B' and (resid 137 through 191 )
5X-RAY DIFFRACTION5chain 'B' and (resid 192 through 264 )
6X-RAY DIFFRACTION6chain 'B' and (resid 265 through 312 )
7X-RAY DIFFRACTION7chain 'B' and (resid 313 through 354 )
8X-RAY DIFFRACTION8chain 'B' and (resid 355 through 433 )
9X-RAY DIFFRACTION9chain 'B' and (resid 434 through 476 )
10X-RAY DIFFRACTION10chain 'A' and (resid 4 through 38 )
11X-RAY DIFFRACTION11chain 'A' and (resid 39 through 96 )
12X-RAY DIFFRACTION12chain 'A' and (resid 97 through 167 )
13X-RAY DIFFRACTION13chain 'A' and (resid 168 through 191 )
14X-RAY DIFFRACTION14chain 'A' and (resid 192 through 264 )
15X-RAY DIFFRACTION15chain 'A' and (resid 265 through 312 )
16X-RAY DIFFRACTION16chain 'A' and (resid 313 through 354 )
17X-RAY DIFFRACTION17chain 'A' and (resid 355 through 435 )
18X-RAY DIFFRACTION18chain 'A' and (resid 436 through 476 )
19X-RAY DIFFRACTION19chain 'C' and (resid 5 through 38 )
20X-RAY DIFFRACTION20chain 'C' and (resid 39 through 96 )
21X-RAY DIFFRACTION21chain 'C' and (resid 97 through 167 )
22X-RAY DIFFRACTION22chain 'C' and (resid 168 through 191 )
23X-RAY DIFFRACTION23chain 'C' and (resid 192 through 281 )
24X-RAY DIFFRACTION24chain 'C' and (resid 282 through 354 )
25X-RAY DIFFRACTION25chain 'C' and (resid 355 through 476 )
26X-RAY DIFFRACTION26chain 'D' and (resid -1 through 38 )
27X-RAY DIFFRACTION27chain 'D' and (resid 39 through 96 )
28X-RAY DIFFRACTION28chain 'D' and (resid 97 through 167 )
29X-RAY DIFFRACTION29chain 'D' and (resid 168 through 191 )
30X-RAY DIFFRACTION30chain 'D' and (resid 192 through 281 )
31X-RAY DIFFRACTION31chain 'D' and (resid 282 through 354 )
32X-RAY DIFFRACTION32chain 'D' and (resid 355 through 476 )

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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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