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- PDB-3igr: The Crystal Structure of Ribosomal-protein-S5-alanine Acetyltrans... -

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Basic information

Entry
Database: PDB / ID: 3igr
TitleThe Crystal Structure of Ribosomal-protein-S5-alanine Acetyltransferase from Vibrio fischeri to 2.0A
ComponentsRibosomal-protein-S5-alanine N-acetyltransferase
KeywordsTRANSFERASE / Ribosomal-protein / alanine / acetyltransferase / vibrio / fischeri / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative / Acyltransferase
Function / homology
Function and homology information


: / ribosomal-protein-alanine N-acetyltransferase / peptide-alanine-alpha-N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribosomal-protein-S5-alanine N-acetyltransferase
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsStein, A.J. / Sather, A. / Shackelford, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of Ribosomal-protein-S5-alanine Acetyltransferase from Vibrio fischeri to 2.0A
Authors: Stein, A.J. / Sather, A. / Shackelford, G. / Joachimiak, A.
History
DepositionJul 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosomal-protein-S5-alanine N-acetyltransferase
B: Ribosomal-protein-S5-alanine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8346
Polymers43,6732
Non-polymers1614
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribosomal-protein-S5-alanine N-acetyltransferase
hetero molecules

A: Ribosomal-protein-S5-alanine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7646
Polymers43,6732
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2580 Å2
ΔGint-53 kcal/mol
Surface area18100 Å2
MethodPISA
3
B: Ribosomal-protein-S5-alanine N-acetyltransferase
hetero molecules

B: Ribosomal-protein-S5-alanine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9036
Polymers43,6732
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area2800 Å2
ΔGint-38 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.504, 107.173, 145.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailsauthor states that the biological unit is the same as asymmetric unit.

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Components

#1: Protein Ribosomal-protein-S5-alanine N-acetyltransferase


Mass: 21836.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: rimJ, VFA0750, VF_A0750 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5DZH6, ribosomal-protein-alanine N-acetyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 10% PEG 20000, 2% Dioxane, 0.1M Bicine pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 34070 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.094 / Χ2: 1.381 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.074.90.733671.0581100
2.07-2.154.90.5433690.9831100
2.15-2.254.90.39733390.9621100
2.25-2.374.90.30533890.9491100
2.37-2.5250.2333800.917199.9
2.52-2.714.90.15933900.973199.9
2.71-2.994.90.11534161.174199.9
2.99-3.424.90.08234131.556199.9
3.42-4.314.80.05134491.732199.9
4.31-504.80.05635583.495198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 2→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.197 / SU B: 9.003 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1728 5.1 %RANDOM
Rwork0.205 ---
obs0.207 34029 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--1.69 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2992 0 8 143 3143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223132
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9134251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57522.893159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.58515514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6451521
X-RAY DIFFRACTIONr_chiral_restr0.0880.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212426
X-RAY DIFFRACTIONr_mcbond_it0.4671.51840
X-RAY DIFFRACTIONr_mcangle_it0.82822962
X-RAY DIFFRACTIONr_scbond_it1.6731292
X-RAY DIFFRACTIONr_scangle_it2.4254.51283
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.997-2.0490.2681120.2432314248397.704
2.049-2.1050.3091420.2412273241899.876
2.105-2.1660.3021230.2282226235399.83
2.166-2.2320.2481070.2132209231999.871
2.232-2.3050.2561020.2182140224799.777
2.305-2.3860.2751080.21420372145100
2.386-2.4760.2641080.2191967207899.856
2.476-2.5770.268860.22819202006100
2.577-2.6920.286930.2231846194199.897
2.692-2.8230.222910.2161764185799.892
2.823-2.9750.284860.2161665175299.943
2.975-3.1550.2261090.2061560167299.821
3.155-3.3730.235840.2051483156899.936
3.373-3.6420.249730.1991408148299.933
3.642-3.9890.17650.1831288135699.779
3.989-4.4580.22730.17111661239100
4.458-5.1450.189590.1661038109899.909
5.145-6.2930.227440.21989794599.577
6.293-8.8670.25450.22169374698.928
8.867-72.9320.18180.20940744595.506
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)
116.13450.8303-1.737213.4149-11.413617.6172-0.49070.1683-2.1076-0.8635-0.1987-0.04831.41690.03380.68940.37520.09080.03680.3512-0.0640.422917.13823.32415.9846
21.9665-3.1617-4.5733-0.62531.716412.6708-0.1827-0.0740.0257-0.15380.1804-0.01610.40440.57870.00220.23110.12560.06170.38810.09670.280922.26935.168520.3272
32.0676-2.33414.700814.03788.09598.0819-0.20730.4475-0.1690.57720.52860.10480.8871.6115-0.32130.39450.54190.13511.05160.19740.187623.9976-1.851431.1922
419.72377.6493-12.585510.44927.397922.1264-0.0815-0.93180.23840.16420.5226-0.24260.62762.1378-0.44110.14050.1469-0.05041.03190.18530.17225.65367.88539.0321
53.9371.7307-4.472317.0392-1.41976.1399-0.2861-0.23830.0409-1.4064-0.0416-0.59230.56411.30370.32770.29530.2150.11890.74450.26480.246918.64188.144643.4053
69.67930.86578.15831.31641.324418.450.1664-0.0287-0.15380.20330.00480.43461.49380.759-0.17120.49220.34010.20520.46790.16780.258520.2564-4.288438.3076
738.5414-22.704912.060914.1104-10.51984.36541.0235-0.4981-1.4684-2.218-0.54441.66021.97310.5438-0.47911.02830.30580.03370.27770.08190.619310.6083-5.363230.084
89.63132.4778-2.64543.0081-0.13675.3143-0.3135-0.0681-0.6289-0.11380.02990.2730.46010.25190.28350.1830.04870.00620.16920.09690.260713.81872.629325.2386
917.9824.3784-6.774612.7661-9.936323.8697-0.3118-0.1518-0.5895-0.45210.1739-0.75430.87381.67580.13790.18710.12590.04690.60520.13510.277230.44393.375822.7968
1026.89812.7157-1.14592.0529-0.84552.7822-0.0101-0.8732-0.41610.1125-0.21240.02790.0730.17870.22250.094-0.0013-0.02860.17770.07850.179810.61026.96228.9569
1113.98190.67450.12120.73560.60773.2352-0.0773-0.53530.00810.0104-0.057-0.12730.03720.45530.13430.10370.0118-0.01880.13520.06830.10989.372110.366429.0462
1212.15492.82272.901115.3079-2.001418.74760.1957-0.9509-0.03410.73810.0746-0.638-0.4081.2647-0.27040.1759-0.02810.00540.3283-0.00130.261723.110516.898323.8926
1336.066811.54247.1944.92467.21738.622-0.09320.7953-0.3713-0.135-0.1208-0.0089-0.1934-0.23790.2140.16480.07760.00190.2440.05080.131810.228211.108219.7927
144.1161-0.7157-0.52392.90983.59573.61370.24890.4475-0.3151-0.37610.0627-0.2805-0.3060.1873-0.31160.16880.0175-0.03830.1549-0.00930.1731.463611.229221.7838
152.1408-0.86796.78845.75810.392734.77860.1193-0.24760.09080.3039-0.65080.37960.3338-1.44660.53150.2113-0.0772-0.00140.23420.04020.19210.043619.472835.633
160.8633-0.92856.86492.8128-0.61232.1095-0.21390.19660.1213-0.04730.2132-1.1113-1.46451.64180.00070.2698-0.2654-0.02510.43980.07650.441716.909122.211432.9787
178.83680.9102-2.88178.9445-0.34368.0340.15660.76170.5571-0.0646-0.3911-0.2198-1.03490.08850.23450.2811-0.0753-0.03920.12720.06970.1558.738922.826326.3445
186.7975-5.71267.73797.3194-8.109511.3492-0.23570.27570.3660.3444-0.1098-0.1392-0.57610.29340.34550.1706-0.0738-0.03170.1269-0.00910.12257.735218.259243.7485
191.81930.5593.94021.4796-0.064510.9851-0.30650.05760.12780.03570.0691-0.0467-0.93390.29530.23740.1218-0.0091-0.0190.09690.01670.13786.983518.687636.7977
2030.348123.1017-3.700333.3976-7.725911.2064-0.11390.8421-0.35730.0062-0.4372-0.5685-0.7051-0.14450.55110.141-0.0171-0.03980.12980.00380.0661-3.948713.149316.1419
212.3399-2.5374-3.926911.317-3.74749.1345-0.0894-0.36950.15120.6424-0.1189-0.4057-0.12330.31220.20830.2783-0.07640.06850.271-0.05270.217321.975430.278217.3925
224.0637-1.5448-1.0757.08063.27867.60510.1294-0.06080.01010.2489-0.0621-0.64440.83530.5542-0.06730.23610.0420.06240.11050.07760.173630.749930.19895.9704
2313.96664.15418.253635.33373.16398.96720.39820.9197-0.406-0.5726-0.6297-0.47281.11350.92440.23140.42590.0050.07020.226-0.00260.130523.506627.0778-3.099
241.87954.0124-1.97296.912-8.781715.87480.5445-0.3298-0.45240.0936-0.1959-0.22020.9138-0.3723-0.34860.3919-0.05170.01930.17210.00080.471918.150633.6273-6.7698
2527.2538-1.207912.69074.6689-12.860317.64950.27050.3031-0.6826-0.3398-0.7007-0.50310.44961.08850.43030.32960.07010.12550.23110.12250.267829.658332.8159-6.9929
2618.61265.9852-1.21217.984814.366713.0916-0.23030.3847-0.24430.53560.9609-0.93020.76021.1013-0.73060.29690.20280.14790.44220.14970.155434.720431.93-1.5492
2729.4592-19.9072-11.331221.093311.788412.01571.21660.83521.2763-1.047-0.6838-0.7625-0.78450.9333-0.53280.2334-0.03760.15460.32660.06810.357135.440139.6432.5379
281.4752-2.4189-11.41520.683115.886217.43770.2106-1.45790.86380.20851.0607-0.6799-0.11012.6717-1.27130.1413-0.0356-0.04780.7452-0.33760.879534.861545.9629.6246
293.8684-1.1704-1.0789.98222.97143.24310.0325-0.09060.3231-0.0812-0.056-0.5421-0.13940.15470.02360.0894-0.0380.02630.1141-0.02070.190426.400339.534710.1914
304.6708-4.03470.550220.5513-16.266215.9605-0.1286-0.1208-0.2835-0.6841-0.4098-0.1011.3460.70530.53830.39550.00890.13850.14480.02930.18723.770422.867110.8838
310.66710.9730.328717.11294.82232.5351-0.07560.20740.1173-0.59730.0538-0.404-0.1941-0.00330.02170.0993-0.03790.03540.1236-0.02250.126621.830150.36017.9649
322.33476.5056-0.873315.2087-0.77497.99560.0350.00120.0655-0.6953-0.03710.38920.2171-0.43170.00210.4539-0.0838-0.0160.0768-0.03250.178216.669131.7813.7528
3334.4585-13.2847-12.965114.82490.8177.4055-0.01781.3532-0.6364-0.9482-0.19530.43340.7802-0.8640.21310.4367-0.1953-0.01220.218-0.05640.194513.127624.05436.5386
3418.72724.729819.122943.597714.357214.4450.7977-0.9035-0.24550.5613-0.72540.55490.5712-1.1279-0.07230.1239-0.09150.01850.23860.06740.331812.875932.438312.9967
353.933611.05573.584229.25389.05451.93610.1961-0.15570.10070.6858-0.2913-0.01830.2258-0.10480.09520.1636-0.0031-0.03430.1908-0.06360.197719.335444.416617.1132
3612.72312.35755.141826.13865.28550.597-0.44140.99070.1589-1.34050.459-0.0019-0.39350.3527-0.01760.1181-0.04590.02920.1676-0.00960.145115.561551.65089.7529
375.90192.46645.97575.16861.100622.2602-0.51470.192-0.3158-0.12160.25280.25220.855-0.81980.26190.1709-0.070.05450.2001-0.09320.15558.24741.0573-2.3575
384.5842-0.18230.72567.19571.808612.1016-0.0972-0.1532-0.5981-0.12590.34990.36561.0058-1.2247-0.25270.2234-0.18950.02830.27260.01660.25246.80639.26396.6662
396.3934-2.2696-6.39331.96531.637710.4353-0.16120.1346-0.20520.115-0.08680.22420.3479-0.45040.2480.1341-0.04710.00010.162-0.03950.10411.321145.8044-8.3321
404.04332.87195.18664.86165.72259.5084-0.0338-0.30850.04350.0797-0.27970.16850.1838-0.72190.31350.0787-0.04170.03270.1341-0.0150.106513.048652.265513.4911
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 6
2X-RAY DIFFRACTION2A7 - 16
3X-RAY DIFFRACTION3A17 - 26
4X-RAY DIFFRACTION4A27 - 35
5X-RAY DIFFRACTION5A36 - 43
6X-RAY DIFFRACTION6A44 - 53
7X-RAY DIFFRACTION7A54 - 63
8X-RAY DIFFRACTION8A64 - 74
9X-RAY DIFFRACTION9A75 - 80
10X-RAY DIFFRACTION10A81 - 90
11X-RAY DIFFRACTION11A91 - 107
12X-RAY DIFFRACTION12A108 - 115
13X-RAY DIFFRACTION13A116 - 125
14X-RAY DIFFRACTION14A126 - 133
15X-RAY DIFFRACTION15A134 - 139
16X-RAY DIFFRACTION16A140 - 148
17X-RAY DIFFRACTION17A149 - 155
18X-RAY DIFFRACTION18A156 - 166
19X-RAY DIFFRACTION19A167 - 179
20X-RAY DIFFRACTION20A180 - 184
21X-RAY DIFFRACTION21B2 - 13
22X-RAY DIFFRACTION22B14 - 26
23X-RAY DIFFRACTION23B27 - 31
24X-RAY DIFFRACTION24B32 - 41
25X-RAY DIFFRACTION25B42 - 46
26X-RAY DIFFRACTION26B47 - 52
27X-RAY DIFFRACTION27B53 - 58
28X-RAY DIFFRACTION28B59 - 64
29X-RAY DIFFRACTION29B65 - 73
30X-RAY DIFFRACTION30B74 - 82
31X-RAY DIFFRACTION31B83 - 99
32X-RAY DIFFRACTION32B100 - 105
33X-RAY DIFFRACTION33B106 - 110
34X-RAY DIFFRACTION34B111 - 116
35X-RAY DIFFRACTION35B117 - 129
36X-RAY DIFFRACTION36B130 - 134
37X-RAY DIFFRACTION37B135 - 140
38X-RAY DIFFRACTION38B141 - 154
39X-RAY DIFFRACTION39B155 - 172
40X-RAY DIFFRACTION40B173 - 184

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