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- PDB-6c8t: The structure of MppP soaked with the substrate L-Arg -

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Basic information

Entry
Database: PDB / ID: 6c8t
TitleThe structure of MppP soaked with the substrate L-Arg
Components(PLP-Dependent L-Arginine Hydroxylase MppP) x 2
KeywordsOXIDOREDUCTASE / dimer / L-Arg binding complex / oxidase / PLP / ANTIBIOTIC
Function / homology
Function and homology information


biosynthetic process / pyridoxal phosphate binding / metal ion binding
Similarity search - Function
Enduracididine biosynthesis enzyme MppP / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / 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 ...Enduracididine biosynthesis enzyme MppP / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / 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
Chem-EQJ / PLP-Dependent L-Arginine Hydroxylase MppP
Similarity search - Component
Biological speciesStreptomyces wadayamensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHan, L. / Silvaggi, N.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1606842 United States
CitationJournal: Biochemistry / Year: 2018
Title: Streptomyces wadayamensis MppP is a PLP-Dependent Oxidase, Not an Oxygenase.
Authors: Han, L. / Vuksanovic, N. / Oehm, S.A. / Fenske, T.G. / Schwabacher, A.W. / Silvaggi, N.R.
History
DepositionJan 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 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
A: PLP-Dependent L-Arginine Hydroxylase MppP
B: PLP-Dependent L-Arginine Hydroxylase MppP
C: PLP-Dependent L-Arginine Hydroxylase MppP
D: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,6258
Polymers166,3794
Non-polymers1,2454
Water13,115728
1
A: PLP-Dependent L-Arginine Hydroxylase MppP
B: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8824
Polymers83,0762
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-32 kcal/mol
Surface area25200 Å2
MethodPISA
2
C: PLP-Dependent L-Arginine Hydroxylase MppP
D: PLP-Dependent L-Arginine Hydroxylase MppP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7424
Polymers83,3042
Non-polymers4392
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-38 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.792, 108.425, 196.219
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PLP-Dependent L-Arginine Hydroxylase MppP


Mass: 41537.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces wadayamensis (bacteria) / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0X1KHF5
#2: Protein PLP-Dependent L-Arginine Hydroxylase MppP


Mass: 41765.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces wadayamensis (bacteria) / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0X1KHF5
#3: Chemical ChemComp-EQJ / (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-arginine


Mass: 403.328 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H22N5O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% polyethylene glycol monomethyl ether 550, 50 mM MgCl2, and 0.1 M HEPES pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 85820 / % possible obs: 91.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 3839 / % possible all: 84.1

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Processing

Software
NameVersionClassification
HKL-2000(1.11.1_2575: ???)data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DJ1
Resolution: 2.2→49.055 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.15
RfactorNum. reflection% reflection
Rfree0.1954 1999 2.33 %
Rwork0.1464 --
obs0.1475 85722 91.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11331 0 82 728 12141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111707
X-RAY DIFFRACTIONf_angle_d1.11915954
X-RAY DIFFRACTIONf_dihedral_angle_d19.8266967
X-RAY DIFFRACTIONf_chiral_restr0.0671806
X-RAY DIFFRACTIONf_plane_restr0.0072098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1991-2.25410.19571280.14325359X-RAY DIFFRACTION84
2.2541-2.3150.20831270.14555342X-RAY DIFFRACTION83
2.315-2.38320.20031300.14475395X-RAY DIFFRACTION83
2.3832-2.46010.21541290.13935418X-RAY DIFFRACTION84
2.4601-2.5480.21921320.14795534X-RAY DIFFRACTION85
2.548-2.650.17281340.1455610X-RAY DIFFRACTION87
2.65-2.77060.20571400.15055834X-RAY DIFFRACTION90
2.7706-2.91670.21441430.14976014X-RAY DIFFRACTION93
2.9167-3.09940.20651490.14486247X-RAY DIFFRACTION96
3.0994-3.33860.18251530.14336389X-RAY DIFFRACTION98
3.3386-3.67450.17291540.12986484X-RAY DIFFRACTION99
3.6745-4.2060.17681580.12756587X-RAY DIFFRACTION100
4.206-5.29810.16771580.13686632X-RAY DIFFRACTION100
5.2981-49.06690.2441640.19196878X-RAY DIFFRACTION100
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)
10.6486-0.0212-0.36590.53510.07351.06720.0572-0.0267-0.2059-0.1443-0.021-0.09330.1831-0.1558-0.05140.31560.00010.02960.16920.05280.278634.6123203.3826223.9368
20.83420.2045-0.17140.2998-0.31330.39950.0135-0.23250.08180.1088-0.0669-0.0918-0.01390.09060.02740.18110.00060.00630.18380.02450.198342.1009220.6173233.9846
31.4353-0.0832-0.34530.55180.23250.7094-0.08840.0717-0.0442-0.16290.0031-0.05440.04280.07280.07860.19540.02210.04620.14550.03030.152945.4688222.0712209.4389
40.8037-0.06960.06251.0979-0.00030.6207-0.0105-0.06870.0065-0.02940.0002-0.22710.04460.18240.00390.13960.02710.0340.17350.0460.266454.9982222.4828218.5178
50.54620.6263-0.35432.7281-0.97890.5494-0.0706-0.1518-0.0408-0.0349-0.0101-0.11310.09870.07480.05890.15480.00190.03210.12610.04890.21841.1459218.4555224.8911
61.2835-0.3407-0.01520.68260.02870.5596-0.0862-0.2271-0.04580.10280.1038-0.0650.0509-0.0751-0.02730.15620.0088-0.01160.15260.03760.15436.5596217.0441231.1494
70.5086-0.0974-0.42980.67080.86782.1692-0.1195-0.0734-0.25590.0051-0.0059-0.27840.24610.125-0.01520.33820.09540.04450.16050.09040.434652.5051196.3085223.034
81.6383-0.4649-0.06482.23250.45080.634-0.03090.0817-0.1466-0.19210.1006-0.34780.11860.1736-0.14080.36680.12720.1240.1830.00910.433255.9413198.639211.0872
90.27460.0867-0.04110.91430.11040.3054-0.04670.2494-0.1741-0.53040.0123-0.11330.22490.0168-0.0230.55080.06530.11850.1898-0.09510.326145.1157200.6096201.6065
100.5468-0.1597-0.00581.25930.49071.188-0.03250.0272-0.3219-0.06580.0328-0.03320.32110.0866-0.03270.44620.07460.10330.11770.01050.463146.55191.6525211.968
111.31940.7884-0.07361.8292-0.0130.7824-0.0573-0.1791-0.0813-0.05070.0032-0.402-0.0108-0.049-0.00610.20940.04830.00450.31680.03180.239223.7312227.889234.2271
120.8115-0.52480.20050.61560.02290.47970.0029-0.0465-0.32230.0113-0.0419-0.01490.2956-0.07030.05040.2758-0.0822-0.00190.16310.06760.254920.646201.9829226.5122
131.39770.1851-0.11340.8238-0.05880.79630.14980.2319-0.062-0.1512-0.091-0.04660.1741-0.1281-0.04340.2002-0.0009-0.0220.14250.00840.163620.8085215.604212.7474
141.9787-0.5745-0.52530.91890.69860.77990.05550.04370.219-0.2366-0.0469-0.1027-0.1008-0.1330.01550.21160.06790.0250.22010.05090.17820.7399232.3335212.9495
151.5399-0.24020.36490.35680.05190.3260.04210.32730.3889-0.2045-0.1384-0.1043-0.1237-0.11660.02620.2650.09530.00530.27960.07130.194612.1976233.496207.9775
160.96170.1856-0.33340.77110.01351.14670.11650.0177-0.0803-0.1597-0.08670.0750.0266-0.3354-0.00940.17180.0146-0.03460.2464-0.00190.16038.2759221.7517211.9692
170.6837-0.1219-0.21570.7848-0.76413.73580.005-0.0145-0.13890.0028-0.0384-0.0056-0.0546-0.1959-0.0070.19990.01080.00060.15370.02570.15519.8536215.3626217.9686
180.7854-0.35-0.10070.5440.00080.8897-0.0126-0.0751-0.256-0.094-0.0476-0.03060.2527-0.17630.07640.2486-0.0722-0.01980.15780.02280.195822.7599208.8132220.5067
190.92180.2380.46314.50210.50110.7249-0.038-0.19470.01490.27760.02550.13890.0895-0.34230.04520.1924-0.02110.04120.45890.02940.18075.5279222.8133237.1533
202.1333-0.8806-0.25894.2970.63212.16950.0305-0.22050.16150.3329-0.02310.3185-0.112-0.32330.02140.16540.07580.04070.3323-0.03120.215.6345234.6905233.0387
210.7496-0.19560.16221.0755-0.28041.849-0.0333-0.18250.36120.1529-0.1156-0.0506-0.62760.0550.0630.2950.0226-0.02460.2564-0.06910.28418.611241.029232.5332
221.57920.0974-0.08182.0703-0.06232.598-0.0032-0.66510.18560.26050.01790.14-0.2403-0.10960.0190.23340.0638-0.01370.4188-0.05780.201413.0922232.8385241.7402
230.4107-0.0941-0.46370.0904-0.06760.9533-0.1305-0.07840.1616-0.07320.0859-0.1807-0.03580.27890.02860.38850.0611-0.00210.3266-0.07830.368552.2661273.4688212.6367
241.2296-0.24040.41310.51530.33930.511-0.0619-0.3518-0.02750.12870.1059-0.0216-0.0467-0.02250.01290.2730.1357-0.00920.3719-0.0930.140450.2824261.1553236.5918
251.2714-0.4965-0.32520.7030.41250.4902-0.0699-0.2011-0.14860.0770.10140.080.0271-0.12840.00830.13380.04360.00540.19480.00770.151946.8085250.4249220.7476
261.3219-0.56130.16720.6531-0.29370.4368-0.04690.02590.1005-0.09850.0689-0.1368-0.0520.0171-0.02910.14740.0086-0.01540.1434-0.01220.134545.2438253.8655204.598
270.1631-0.0821-0.04440.9910.05510.8901-0.0555-0.2023-0.00110.00980.1310.2743-0.0199-0.3337-0.01430.11090.0580.00990.24810.01090.194233.5044253.0698212.865
280.44260.42690.40623.11121.56050.9404-0.1017-0.2620.02410.16410.07430.0677-0.0372-0.16910.06140.16720.07280.00460.2278-0.03850.183346.6913255.9122222.21
290.6537-0.109-0.02790.72620.44030.5074-0.1161-0.377-0.02820.10150.12720.0107-0.1255-0.0787-0.04260.22790.10040.00910.2616-0.05280.118750.617256.6982229.0109
300.13170.15690.00590.3681-0.53271.6368-0.0769-0.11540.0810.10120.06480.1342-0.2168-0.0903-0.12180.36320.1811-0.01490.2535-0.11420.312935.5089278.6652220.3847
311.2885-0.4606-0.13311.5717-0.0160.66570.00440.02920.0514-0.05910.01720.1646-0.1483-0.0868-0.03580.38330.1758-0.09280.207-0.07590.308933.2782276.3921208.7697
320.37250.78530.08142.25980.37570.75490.06280.2520.1803-0.61240.2145-0.2966-0.5163-0.0719-0.10040.40090.03270.08180.17690.02780.300844.8001275.6552200.2412
330.5415-0.26550.11311.4907-0.34950.91330.0124-0.09910.2702-0.01330.1494-0.1038-0.3396-0.0960.02590.42220.11810.03550.1349-0.04550.348742.5716283.6692211.0816
341.0736-1.09760.31751.59720.0130.7011-0.1618-0.33160.08650.0910.11680.1445-0.14610.13590.07160.26530.04210.01920.3538-0.12920.20665.0195262.6936234.9996
351.0211-0.2671-0.21350.62760.2230.8459-0.025-0.11590.0946-0.03930.0035-0.0429-0.11530.16450.0290.1477-0.02280.00630.1608-0.0210.136872.751255.1265214.154
360.74950.16030.10911.98370.70350.7912-0.0302-0.4167-0.1050.22960.0432-0.17820.05430.19950.0030.15290.0504-0.03460.46130.02980.162981.0166243.8805235.1371
370.5440.0669-0.21041.14060.20381.2220.1228-0.4948-0.27880.2184-0.0822-0.05960.201-0.2776-0.04860.23090.00320.0070.46680.14490.260570.1792235.0326234.5425
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 54 )
2X-RAY DIFFRACTION2chain 'A' and (resid 55 through 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 218 )
5X-RAY DIFFRACTION5chain 'A' and (resid 219 through 242 )
6X-RAY DIFFRACTION6chain 'A' and (resid 243 through 272 )
7X-RAY DIFFRACTION7chain 'A' and (resid 273 through 291 )
8X-RAY DIFFRACTION8chain 'A' and (resid 292 through 313 )
9X-RAY DIFFRACTION9chain 'A' and (resid 314 through 349 )
10X-RAY DIFFRACTION10chain 'A' and (resid 350 through 375 )
11X-RAY DIFFRACTION11chain 'B' and (resid 8 through 35 )
12X-RAY DIFFRACTION12chain 'B' and (resid 36 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 103 )
14X-RAY DIFFRACTION14chain 'B' and (resid 104 through 124 )
15X-RAY DIFFRACTION15chain 'B' and (resid 125 through 156 )
16X-RAY DIFFRACTION16chain 'B' and (resid 157 through 218 )
17X-RAY DIFFRACTION17chain 'B' and (resid 219 through 242 )
18X-RAY DIFFRACTION18chain 'B' and (resid 243 through 272 )
19X-RAY DIFFRACTION19chain 'B' and (resid 273 through 291 )
20X-RAY DIFFRACTION20chain 'B' and (resid 292 through 313 )
21X-RAY DIFFRACTION21chain 'B' and (resid 314 through 349 )
22X-RAY DIFFRACTION22chain 'B' and (resid 350 through 375 )
23X-RAY DIFFRACTION23chain 'C' and (resid 8 through 35 )
24X-RAY DIFFRACTION24chain 'C' and (resid 36 through 72 )
25X-RAY DIFFRACTION25chain 'C' and (resid 73 through 103 )
26X-RAY DIFFRACTION26chain 'C' and (resid 104 through 127 )
27X-RAY DIFFRACTION27chain 'C' and (resid 128 through 218 )
28X-RAY DIFFRACTION28chain 'C' and (resid 219 through 242 )
29X-RAY DIFFRACTION29chain 'C' and (resid 243 through 272 )
30X-RAY DIFFRACTION30chain 'C' and (resid 273 through 292 )
31X-RAY DIFFRACTION31chain 'C' and (resid 293 through 313 )
32X-RAY DIFFRACTION32chain 'C' and (resid 314 through 349 )
33X-RAY DIFFRACTION33chain 'C' and (resid 350 through 375 )
34X-RAY DIFFRACTION34chain 'D' and (resid 22 through 54 )
35X-RAY DIFFRACTION35chain 'D' and (resid 55 through 272 )
36X-RAY DIFFRACTION36chain 'D' and (resid 273 through 313 )
37X-RAY DIFFRACTION37chain 'D' and (resid 314 through 375 )

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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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