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- PDB-3f0n: Mus Musculus Mevalonate Pyrophosphate Decarboxylase -

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Basic information

Entry
Database: PDB / ID: 3f0n
TitleMus Musculus Mevalonate Pyrophosphate Decarboxylase
ComponentsMEVALONATE PYROPHOSPHATE DECARBOXYLASEDiphosphomevalonate decarboxylase
KeywordsLYASE / CHOLESTEROL BIOSYNTHESIS / LIPID SYNTHESIS / STEROID BIOSYNTHESIS / STEROL BIOSYNTHESIS / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


Cholesterol biosynthesis / Synthesis of Dolichyl-phosphate / diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / isoprenoid biosynthetic process / cholesterol biosynthetic process / peroxisomal matrix / Hsp70 protein binding / peroxisome ...Cholesterol biosynthesis / Synthesis of Dolichyl-phosphate / diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / isoprenoid biosynthetic process / cholesterol biosynthetic process / peroxisomal matrix / Hsp70 protein binding / peroxisome / positive regulation of cell population proliferation / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWalker, J.R. / Davis, T. / Vesterberg, A. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Structure of Mus Musculus Mevalonate Pyrophosphate Decarboxylase
Authors: Walker, J.R. / Davis, T. / Vesterberg, A. / Li, Y. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionOct 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEVALONATE PYROPHOSPHATE DECARBOXYLASE
B: MEVALONATE PYROPHOSPHATE DECARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8134
Polymers91,6232
Non-polymers1902
Water7,927440
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-30 kcal/mol
Surface area31120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.619, 139.619, 88.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein MEVALONATE PYROPHOSPHATE DECARBOXYLASE / Diphosphomevalonate decarboxylase / DIPHOSPHOMEVALONATE DECARBOXYLASE


Mass: 45811.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MVD / Plasmid: PET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)V2R
References: UniProt: Q99JF5, diphosphomevalonate decarboxylase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 17 MG/ML PROTEIN, 20% PEG 3350, 0.2M AMMONIUM PHOSPHATE, 0.1M SODIUM/POTASSIUM PHOSPHATE BUFFER, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 4, 2008
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 69315 / Num. obs: 69315 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11 % / Rmerge(I) obs: 0.12
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.37 / Num. unique all: 6822 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
REFMAC5.5.0063refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FI4
Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.369 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 3499 5.1 %RANDOM
Rwork0.18171 ---
obs0.18369 65736 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5900 0 10 443 6353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226033
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9528218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7735770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68923.84263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.315967
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3451542
X-RAY DIFFRACTIONr_chiral_restr0.0870.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214581
X-RAY DIFFRACTIONr_mcbond_it0.6621.53838
X-RAY DIFFRACTIONr_mcangle_it1.14126189
X-RAY DIFFRACTIONr_scbond_it232195
X-RAY DIFFRACTIONr_scangle_it3.2564.52029
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 245 -
Rwork0.247 4758 -
obs--99.88 %
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)
10.9323-0.52761.1680.6111-0.11372.657-0.1433-0.05380.09760.08350.0778-0.0078-0.11940.1780.06550.07560.023-0.03790.1626-0.06490.119649.4109-1.31923.9366
20.4105-0.3886-0.04930.81290.36721.8939-0.0781-0.1440.01240.01030.1396-0.01650.03530.0244-0.06160.04340.0358-0.02370.1219-0.04240.093748.4628-4.393523.0526
34.1673-3.22122.48939.7243-5.09516.0071-0.2157-0.4568-0.23380.52960.16740.04130.08-0.09280.04820.20310.07720.05620.2528-0.03550.070345.4868-10.804247.1061
41.7407-0.3721-0.96021.41662.60144.83850.0659-0.0494-0.28360.4484-0.15670.01980.835-0.33870.09080.3783-0.0298-0.00240.29590.08770.068340.113-18.642541.1077
510.09570.99523.43383.4368-0.20834.0124-0.01350.0017-0.3716-0.07070.0394-0.240.36160.1441-0.02590.21470.05970.00840.1893-0.00290.122455.6355-18.125937.3106
66.2401-3.33413.0354.8916-0.23882.11720.2313-0.2343-0.1680.3431-0.0171-0.23130.4093-0.1536-0.21420.43830.18310.01520.2750.05820.051550.7327-16.214647.5474
710.5799-0.35489.62270.0162-0.32088.75520.4945-0.1249-0.6277-0.00780.02950.05640.4352-0.1405-0.5240.15670.06170.03840.3998-0.0840.370236.1163-2.944731.138
82.7417-0.0921.09450.54880.226.5134-0.2171-0.1835-0.23260.3230.1775-0.02840.2060.22880.03960.21160.1396-0.0150.1697-0.040.059553.7449-9.001438.5491
90.6626-1.3480.21413.2836-0.23110.7599-0.1773-0.17570.05630.16220.2766-0.12590.11490.0569-0.09930.18940.105-0.03810.1859-0.06880.062951.859-5.213328.742
104.2984-1.3328-0.61814.48840.21643.8287-0.0708-0.03450.11850.10960.2202-0.53380.15650.5129-0.14940.04630.0709-0.04340.163-0.09340.12959.9408-8.207122.9113
113.60610.18111.26430.8123-0.40540.7438-0.1131-0.10340.15230.09980.0789-0.0248-0.106-0.02850.03430.10080.029-0.04780.1328-0.10610.106848.337311.827.6796
123.6743-3.5808-1.71559.67343.91291.6147-0.2051-0.1645-0.4399-0.1234-0.17660.9555-0.0224-0.05530.38170.11390.0077-0.00210.27710.03020.184430.3847-5.622220.7462
132.0250.7671-0.22351.8817-0.15711.4339-0.0331-0.0392-0.0784-0.18510.0711-0.06690.20180.0499-0.0380.08280.011-0.02250.0859-0.03270.081347.8889-10.23239.6994
140.75440.29240.35821.05710.38320.8013-0.0194-0.07230.0631-0.08520.0297-0.0574-0.04730.0371-0.01030.05870.0003-0.01990.086-0.03740.090444.32452.813312.964
153.58551.3483-1.74965.4529-1.46082.805-0.0260.03850.2005-0.1692-0.04160.154-0.1939-0.13090.06760.0930.0257-0.06810.0896-0.04770.127334.199115.38311.6936
161.03330.07540.30241.55090.31550.944-0.0967-0.11320.1520.11980.06090.0298-0.0851-0.01120.03580.06460.0284-0.03350.1079-0.06520.113137.132311.85720.2211
179.2941-0.80543.11561.2774-2.61845.6177-0.2156-0.78830.27310.24260.26870.0364-0.4936-0.6274-0.05310.1120.1223-0.01890.2046-0.11250.175124.391912.404924.9778
183.1004-0.6656-1.46484.00030.15590.7474-0.02640.20160.2515-0.17130.0740.4322-0.0881-0.2022-0.04760.27160.2276-0.20570.2313-0.14450.240426.691519.612818.7473
190.4198-0.53480.5381.2338-0.22491.5228-0.2042-0.27620.04660.43820.19580.05670.0172-0.2990.00830.20670.1124-0.01080.3288-0.10110.088239.9852.385639.4536
2010.44384.78183.17833.64115.276911.2625-0.1287-0.44660.00910.1337-0.11440.14390.2969-0.14810.24310.410.04990.13810.46210.07410.119337.8354-13.268552.9678
211.23540.34040.7090.56970.27721.0631-0.03920.10210.1439-0.112-0.03170.1123-0.206-0.02120.07090.11250.0126-0.02580.0798-0.01510.109927.7446-0.5071-20.3084
228.113-1.13120.50253.48940.5950.1662-0.1696-0.10860.49460.09160.06090.2642-0.0180.00060.10870.20690.0289-0.06330.0160.00160.207323.238812.5777-21.7646
233.2477-2.1642-1.30252.71411.14056.61450.34930.36370.55-0.4223-0.213-0.8328-0.49260.2438-0.13630.26550.01130.05090.21810.03550.300334.28987.7227-33.2867
2410.4316-11.5191-4.674712.80065.122.2560.7534-0.09560.2399-1.1583-0.1625-0.1648-0.49050.2153-0.59090.8729-0.03870.0840.5894-0.2240.870727.906510.0944-39.0449
253.7622-3.4212-0.33297.3959-1.04410.46140.1508-0.41190.15450.8238-0.00410.4608-0.33140.1745-0.14670.32-0.09130.02030.1491-0.04180.245519.07452.6291-18.2541
263.98250.0971.79061.1349-0.23552.62380.02680.31120.0722-0.1706-0.04180.0318-0.18490.18350.0150.11940.0039-0.03080.084-0.00190.096630.02940.6276-26.5745
270.81361.33150.08122.25230.38861.0805-0.02860.0377-0.149-0.10210.0634-0.2268-0.07810.0436-0.03480.10460.0091-0.02710.1024-0.02120.114433.8914-9.1941-19.5523
281.33831.29380.1092.77190.02421.139-0.03540.1185-0.1831-0.2261-0.0034-0.1985-0.02880.15140.03870.0758-0.0082-0.01570.0987-0.02730.088137.359-11.2611-21.3593
291.35560.27510.15292.72031.43921.6955-0.075-0.11380.19330.02280.02140.0995-0.0583-0.13720.05360.07860.007-0.04840.1046-0.03590.109421.9058-6.7269-3.3368
301.0982-0.60220.42772.80520.21691.86-0.03380.06860.0937-0.07070.0007-0.1722-0.19830.15370.03310.0774-0.0314-0.02020.0726-0.01520.091843.47761.5053-3.7736
311.23571.79251.67234.37611.41052.84610.08860.0644-0.11740.0292-0.0061-0.29550.18530.1551-0.08250.07980.0435-0.02040.0976-0.02790.139841.7499-17.8174-10.5194
321.40980.74750.05894.0222.22032.73670.0841-0.0592-0.16220.085-0.0388-0.03980.25840.0134-0.04530.0933-0.0026-0.04670.0745-0.01050.097134.7973-19.1308-5.4325
330.8847-0.01930.34621.41120.3720.66370.0172-0.10290.0497-0.0548-0.04270.0308-0.053-0.10760.02550.08790.0005-0.02940.0821-0.03020.089337.31521.13312.3111
340.9227-0.46030.05789.82330.6081.39680.0701-0.1596-0.04050.2187-0.10920.07730.1889-0.16860.03910.0769-0.0485-0.0260.1074-0.01660.06525.6936-14.96856.9654
350.34180.17940.38460.41420.86371.87210.0297-0.022-0.0209-0.0273-0.05730.04410.0114-0.13020.02760.0921-0.0206-0.03580.0847-0.02470.116127.1116-11.1171-1.4837
364.36810.3007-1.65641.63690.8262.0960.0771-0.04590.0386-0.0006-0.0310.16810.3253-0.294-0.04610.146-0.1057-0.05010.13120.00040.099918.5026-19.9182-1.1438
370.7674-0.45611.78822.8871-0.20247.00370.1361-0.3069-0.0102-0.0331-0.20010.36330.0203-0.90430.0640.0635-0.06920.02330.2545-0.08520.127910.7484-15.65470.1077
383.6503-0.2489-0.03846.038-0.70123.89690.3521-1.65940.22751.2906-0.39970.27650.3428-0.50430.04770.3866-0.34840.09620.887-0.14020.034516.4571-18.836612.0884
390.26320.05770.57710.3139-0.42562.3085-0.0418-0.09620.0982-0.047-0.03460.1009-0.0243-0.24230.07640.07320.0132-0.05160.1273-0.05150.132617.7919-9.807-15.0083
402.82140.23750.07349.24812.19993.75330.04410.12690.06440.0408-0.15540.6020.064-0.51720.11130.15330.0487-0.05890.1891-0.01670.22389.81194.3579-29.7617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-3 - 1711 - 31
2X-RAY DIFFRACTION2AA18 - 4832 - 62
3X-RAY DIFFRACTION3AA49 - 5963 - 73
4X-RAY DIFFRACTION4AA60 - 7874 - 92
5X-RAY DIFFRACTION5AA79 - 9293 - 106
6X-RAY DIFFRACTION6AA100 - 116114 - 130
7X-RAY DIFFRACTION7AA117 - 128131 - 142
8X-RAY DIFFRACTION8AA129 - 152143 - 166
9X-RAY DIFFRACTION9AA153 - 168167 - 182
10X-RAY DIFFRACTION10AA169 - 184183 - 198
11X-RAY DIFFRACTION11AA185 - 200199 - 214
12X-RAY DIFFRACTION12AA201 - 211215 - 225
13X-RAY DIFFRACTION13AA212 - 234226 - 248
14X-RAY DIFFRACTION14AA235 - 282249 - 296
15X-RAY DIFFRACTION15AA283 - 297297 - 311
16X-RAY DIFFRACTION16AA298 - 326312 - 340
17X-RAY DIFFRACTION17AA327 - 341341 - 355
18X-RAY DIFFRACTION18AA342 - 364356 - 378
19X-RAY DIFFRACTION19AA365 - 391379 - 405
20X-RAY DIFFRACTION20AA392 - 397406 - 411
21X-RAY DIFFRACTION21BB7 - 6221 - 76
22X-RAY DIFFRACTION22BB63 - 8377 - 97
23X-RAY DIFFRACTION23BB84 - 9198 - 105
24X-RAY DIFFRACTION24BB92 - 110106 - 124
25X-RAY DIFFRACTION25BB111 - 128125 - 142
26X-RAY DIFFRACTION26BB129 - 160143 - 174
27X-RAY DIFFRACTION27BB161 - 171175 - 185
28X-RAY DIFFRACTION28BB172 - 193186 - 207
29X-RAY DIFFRACTION29BB194 - 209208 - 223
30X-RAY DIFFRACTION30BB210 - 232224 - 246
31X-RAY DIFFRACTION31BB233 - 244247 - 258
32X-RAY DIFFRACTION32BB245 - 261259 - 275
33X-RAY DIFFRACTION33BB262 - 276276 - 290
34X-RAY DIFFRACTION34BB277 - 297291 - 311
35X-RAY DIFFRACTION35BB298 - 311312 - 325
36X-RAY DIFFRACTION36BB312 - 328326 - 342
37X-RAY DIFFRACTION37BB329 - 351343 - 365
38X-RAY DIFFRACTION38BB352 - 365366 - 379
39X-RAY DIFFRACTION39BB366 - 383380 - 397
40X-RAY DIFFRACTION40BB384 - 397398 - 411

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  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
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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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