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- PDB-2p9m: Crystal structure of conserved hypothetical protein MJ0922 from M... -

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Basic information

Entry
Database: PDB / ID: 2p9m
TitleCrystal structure of conserved hypothetical protein MJ0922 from Methanocaldococcus jannaschii DSM 2661
ComponentsHypothetical protein MJ0922Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MJ0922 / Methanocaldococcus jannaschii / SOUTHEAST COLLABORATORY FOR STRUCTURAL GENOMICS / SECSG / Protein Structure Initiative / RIKEN Structural Genomics/Proteomics Initiative / RSGI / PSI
Function / homologyCBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta / Uncharacterized protein MJ0922
Function and homology information
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.59 Å
AuthorsZhao, M. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhu, J. / Swindell II, J.T. / Chen, L. / Fu, Z.-Q. / Charz, J. ...Zhao, M. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhu, J. / Swindell II, J.T. / Chen, L. / Fu, Z.-Q. / Charz, J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of conserved hypothetical protein MJ0922 from Methanocaldococcus jannaschii DSM 2661
Authors: Zhao, M. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhu, J. / Swindell II, J.T. / Chen, L. / Fu, Z.-Q. / Charz, J. / Rose, J.P. / Wang, B.-C.
History
DepositionMar 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 13, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / refine / software / Item: _refine.pdbx_method_to_determine_struct
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein MJ0922
B: Hypothetical protein MJ0922
C: Hypothetical protein MJ0922
D: Hypothetical protein MJ0922


Theoretical massNumber of molelcules
Total (without water)62,9074
Polymers62,9074
Non-polymers00
Water39622
1
A: Hypothetical protein MJ0922
B: Hypothetical protein MJ0922


Theoretical massNumber of molelcules
Total (without water)31,4532
Polymers31,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-20 kcal/mol
Surface area13920 Å2
MethodPISA
2
C: Hypothetical protein MJ0922
D: Hypothetical protein MJ0922


Theoretical massNumber of molelcules
Total (without water)31,4532
Polymers31,4532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-20 kcal/mol
Surface area13950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.207, 94.688, 102.042
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
Hypothetical protein MJ0922 / Hypothesis


Mass: 15726.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Species: Methanocaldococcus jannaschii / Strain: DSM 2661, JAL-1, JCM 10045, NBRC 100440 / Gene: MJ0922 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL-X / References: UniProt: Q58332
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.23 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 289 K / Method: microbatch under oil / pH: 6.3
Details: USING 1.0 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (27.49 mg/ml) AND SOLUTION CONTAINING 27.5% w/v PEG 4000, 0.1 M MES-SODIUM HYDROXIDE, pH 6.3, MICROBATCH UNDER OIL, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9724 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 31, 2007 / Details: ROSENBAUM
RadiationMonochromator: SI CHANNEL 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionRedundancy: 12.6 % / Av σ(I) over netI: 16.7 / Number: 224283 / Rmerge(I) obs: 0.071 / Χ2: 1.65 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 17759 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.65098.710.0583.15612.7
4.455.610010.0612.70713.9
3.884.4599.910.0572.66214
3.533.8810010.0692.07814
3.283.5310010.0831.413.6
3.083.2810010.1060.94713.1
2.933.0810010.160.69812.6
2.82.9399.910.2290.59711.9
2.692.899.410.2970.59910.8
2.62.6996.310.3820.6439.3
ReflectionResolution: 2.59→50 Å / Num. obs: 17759 / % possible obs: 99.4 % / Redundancy: 12.6 % / Rsym value: 0.071 / Net I/σ(I): 16.7
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 4.73 / Rsym value: 0.382 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SGXPROphasing
RefinementMethod to determine structure: SAD / Resolution: 2.59→36.47 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.872 / SU B: 30.587 / SU ML: 0.301 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.003 / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29177 907 5.1 %RANDOM
Rwork0.22193 ---
obs0.22544 17711 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.576 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--1.87 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.59→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4021 0 0 22 4043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223865
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9675251
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06227.424132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.62915676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.953155
X-RAY DIFFRACTIONr_chiral_restr0.0970.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022712
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.21737
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22787
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.214
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.621.52641
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.94524197
X-RAY DIFFRACTIONr_scbond_it1.23831350
X-RAY DIFFRACTIONr_scangle_it1.8994.51050
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.59→2.656 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 65 -
Rwork0.325 1094 -
obs--90.41 %
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)
17.4875-0.43984.61911.6503-5.503119.6996-0.24651.6411-0.1697-0.5447-0.79430.03231.3448-1.03941.04080.26340.1363-0.01560.36130.06550.12851.749160.45911.7344
22.59040.194-1.84846.4927-5.653611.43510.0775-0.70950.24130.90370.14660.2944-0.9648-0.7925-0.22410.3590.10630.04850.3375-0.00990.16072.978259.817337.8076
39.5939-3.20163.0335.7642.02524.292-0.0335-0.4948-0.3420.2296-0.1780.2811-0.7597-0.43070.21140.37670.0407-0.0120.13270.06190.1394.644352.659636.765
414.7154-16.11826.356125.2308-4.57378.4355-0.1769-0.28460.8319-0.18270.0993-0.9238-0.7276-0.1850.07760.3686-0.04970.03390.1517-0.00310.210410.468959.943236.0384
57.5876-6.93024.721912.4872-0.05165.8876-0.5708-0.75510.96380.6521-0.2653-1.9057-0.71591.56130.83610.3021-0.0845-0.08380.52210.13360.319715.254458.284844.6678
67.8204-0.38344.5688.12753.157429.732-0.4422-0.04850.63510.1424-0.5725-0.2297-1.52620.12031.01480.2864-0.0202-0.0141-0.01130.10290.23698.133165.870520.7883
726.93195.10010.48979.78468.470912.58720.62841.02072.5508-0.9357-0.56420.0128-0.70921.5264-0.06420.2213-0.03550.19360.10670.21520.508313.478361.5516.0485
83.261-9.1161-8.665660.201117.28424.4150.2574-1.2424-0.55780.67210.8344-2.99190.85161.8018-1.09180.35820.0008-0.16250.36520.00860.450811.976858.651324.0281
97.1185-5.2804-3.444322.188814.295120.95430.38630.43570.0283-0.4537-0.80910.0994-0.5935-0.9340.42280.17170.0516-0.0290.20430.07420.14353.31859.197719.3329
104.3526-0.35491.01756.6078-7.241318.4868-0.05410.0121-0.3665-0.1466-0.5366-0.7804-0.10630.89450.5907-0.05650.07530.01670.07780.0010.349820.393138.832121.4758
113.0671-1.8422-2.57785.24231.9673.49760.0951-0.1372-0.5355-0.14560.1661-0.07750.00260.2217-0.26130.2403-0.0319-0.04440.22510.07450.279115.989437.395331.2739
129.2521-9.4948-6.580216.08455.75294.8376-0.9346-0.6829-0.86241.79050.31311.15750.5921-1.00810.62150.24780.03510.00620.27210.14660.38658.435333.020139.9167
135.6217-3.66610.15213.9048-9.02217.32260.46420.5785-0.8432-1.4115-0.17670.18561.3595-0.9779-0.28750.1213-0.0127-0.06480.2163-0.05830.202113.772536.900613.6305
1424.8930.0414-27.7912124.864774.662775.7265-0.4567-0.11450.08835.6384-0.38274.03791.5339-2.55350.83940.1530.06860.03180.48970.3350.80796.552641.223614.0824
1527.8486-24.09651.922637.5126-19.820219.91720.7524-0.4022-0.8925-0.4295-0.33370.0719-0.6495-0.3303-0.4187-0.1365-0.1302-0.00310.2992-0.01560.361316.3137.900918.2349
169.5971-12.4222-0.444626.668-7.28457.73860.55360.3255-0.1054-0.7641-0.48-0.8307-0.08190.0678-0.07360.112-0.0473-0.00620.25780.05230.316819.125644.151914.9381
1712.345-0.6845-2.08220.23422.496929.2565-0.4272-0.5096-0.46160.6803-0.2276-0.02480.7291-1.54620.65480.1685-0.07210.03970.11340.01380.148832.364428.307253.6314
182.5606-1.86031.59775.4704-10.050420.1830.580.5235-0.1272-0.5108-0.10670.86280.3243-1.1489-0.47330.13990.0069-0.10210.3646-0.14080.223732.598833.01928.577
192.60091.9561-0.238620.1111-3.58291.96170.01640.2004-0.1478-0.2679-0.1630.8740.4443-0.71830.14650.18370.01170.03250.3675-0.02890.21633.407235.961829.566
2012.11412.6195-1.079919.3478-5.02962.5546-0.2286-0.1226-0.2348-0.5086-0.2943-1.00310.0141-0.21780.52290.2930.08010.01160.3044-0.03850.179243.406237.410429.7622
210.6825-1.27955.657214.07342.542961.7048-0.73230.3111-0.3875-3.02050.8971-1.48911.1917-0.5771-0.16480.5232-0.1510.310.57740.03510.649646.550841.94219.5206
2213.73311.574911.01345.70522.629613.54980.05160.8368-0.0681-0.7371-0.4692-1.61950.93681.04330.41760.24270.04160.110.2919-0.10440.21342.926131.202124.267
237.79191.4234-0.65816.164310.249424.38270.03130.053-1.05090.4086-0.2237-0.28591.09880.43130.19240.18590.07820.01290.05930.04940.242539.950626.220346.6938
2430.335624.08918.862132.0847.862719.62180.0512-1.2136-1.4522-0.4726-0.1869-1.6088-0.19440.04730.13570.28620.05040.13920.2996-0.0050.19937.705327.778541.5603
252.8227-1.56323.778321.154415.904521.02150.0912-0.2667-0.2194-0.6001-0.20430.47650.1916-0.37250.11310.0833-0.04680.05240.30660.04860.168133.156628.019840.6813
266.7295-9.577-17.599530.35838.470562.45220.6649-0.10440.79430.4116-0.43070.5463-0.5157-1.9052-0.23420.136-0.0860.0810.3269-0.09380.216834.124938.719954.5092
270.023-0.72810.116223.0754-3.03096.6711-0.702-1.3173-0.13141.63020.0765-1.24930.73121.19350.62550.18290.0256-0.12440.56280.11030.11749.929344.39860.0326
283.58882.2992-2.49473.43153.17813.38230.3814-0.70740.934-1.2302-0.2945-0.4374-0.73910.9134-0.08680.39250.04360.14960.25530.06130.296149.091758.323438.5772
2918.1097-6.11169.80268.3471-4.627813.26010.79270.5540.4238-0.0331-0.6188-0.3614-0.24920.4995-0.17390.20290.12140.04030.19180.07710.136648.061851.366631.0856
303.66262.10732.58173.5983.488411.3470.0851-0.53920.82190.57-0.30040.5365-0.7118-0.06030.21540.39190.08520.04840.09-0.00960.367942.809756.876339.4311
3134.460411.917418.7421.898711.048811.36480.4587-2.30811.0451-1.9188-1.69450.7499-1.7407-3.69931.23580.37480.47240.11420.52850.05780.143136.567761.180632.0296
324.8307-1.9714-1.6418.9153-5.51820.02110.4819-0.61210.8132.177-0.70890.6279-1.1136-0.21820.22710.09950.03450.09080.2321-0.11420.035543.833851.84456.7742
3325.288421.574719.537418.629216.130316.39320.0391-1.14640.7213-1.88190.79080.3119-0.3334-0.9907-0.830.29490.13850.13630.5210.26730.648235.854948.753854.3948
346.5166-4.81024.150410.8837-4.386426.27431.0245-0.1123-0.35161.49240.03080.6314-0.3246-0.3109-1.05530.1760.01150.09060.2603-0.00540.215145.345552.682550.2745
355.70199.2547-0.641830.3953-2.6757.14090.476-0.703-0.11630.4225-0.5664-1.1645-0.19540.38380.09050.13840.08-0.00440.3812-0.05940.225748.552346.213252.6499
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 145 - 14
2X-RAY DIFFRACTION2AA15 - 2915 - 29
3X-RAY DIFFRACTION3AA30 - 4530 - 45
4X-RAY DIFFRACTION4AA46 - 6546 - 65
5X-RAY DIFFRACTION5AA66 - 8066 - 80
6X-RAY DIFFRACTION6AA81 - 9381 - 93
7X-RAY DIFFRACTION7AA94 - 10094 - 100
8X-RAY DIFFRACTION8AA101 - 113101 - 113
9X-RAY DIFFRACTION9AA114 - 137114 - 137
10X-RAY DIFFRACTION10BB4 - 304 - 30
11X-RAY DIFFRACTION11BB31 - 6431 - 64
12X-RAY DIFFRACTION12BB65 - 7965 - 79
13X-RAY DIFFRACTION13BB80 - 9680 - 96
14X-RAY DIFFRACTION14BB97 - 10897 - 108
15X-RAY DIFFRACTION15BB109 - 116109 - 116
16X-RAY DIFFRACTION16BB117 - 137117 - 137
17X-RAY DIFFRACTION17CC4 - 144 - 14
18X-RAY DIFFRACTION18CC15 - 2815 - 28
19X-RAY DIFFRACTION19CC29 - 5029 - 50
20X-RAY DIFFRACTION20CC51 - 6451 - 64
21X-RAY DIFFRACTION21CC65 - 7265 - 72
22X-RAY DIFFRACTION22CC73 - 8173 - 81
23X-RAY DIFFRACTION23CC82 - 10082 - 100
24X-RAY DIFFRACTION24CC101 - 117101 - 117
25X-RAY DIFFRACTION25CC118 - 128118 - 128
26X-RAY DIFFRACTION26CC129 - 137129 - 137
27X-RAY DIFFRACTION27DD4 - 144 - 14
28X-RAY DIFFRACTION28DD15 - 2815 - 28
29X-RAY DIFFRACTION29DD29 - 3829 - 38
30X-RAY DIFFRACTION30DD39 - 6539 - 65
31X-RAY DIFFRACTION31DD66 - 8166 - 81
32X-RAY DIFFRACTION32DD82 - 9682 - 96
33X-RAY DIFFRACTION33DD97 - 10197 - 101
34X-RAY DIFFRACTION34DD109 - 116109 - 116
35X-RAY DIFFRACTION35DD117 - 137117 - 137

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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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