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- PDB-9f8j: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 9f8j
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with (3-Bromophenyl)[6-hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl]methanone
ComponentsPhenazine biosynthesis protein A/B
KeywordsBIOSYNTHETIC PROTEIN / pyocyanin / phenazine biosynthesis / virulence / inhibitor / ketosteroid-isomerase / cocrystal / PhzA/B / Burkholderia cepacia
Function / homologyPhenazine biosynthesis protein A/B / Phenazine biosynthesis protein A/B / antibiotic biosynthetic process / NTF2-like domain superfamily / : / Phenazine biosynthesis protein A/B
Function and homology information
Biological speciesBurkholderia lata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsThiemann, M. / Zimmermann, M. / Kunick, C. / Blankenfeldt, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: From Bones to Bugs: Structure-Based Development of Raloxifene-Derived Pathoblockers That Inhibit Pyocyanin Production in Pseudomonas aeruginosa.
Authors: Thiemann, M. / Zimmermann, M. / Diederich, C. / Zhan, H. / Lebedev, M. / Pletz, J. / Baumgarten, J. / Handke, M. / Musken, M. / Breinbauer, R. / Krasteva-Christ, G. / Zanin, E. / Empting, M. ...Authors: Thiemann, M. / Zimmermann, M. / Diederich, C. / Zhan, H. / Lebedev, M. / Pletz, J. / Baumgarten, J. / Handke, M. / Musken, M. / Breinbauer, R. / Krasteva-Christ, G. / Zanin, E. / Empting, M. / Schiedel, M. / Kunick, C. / Blankenfeldt, W.
History
DepositionMay 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenazine biosynthesis protein A/B
B: Phenazine biosynthesis protein A/B
C: Phenazine biosynthesis protein A/B
D: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,25119
Polymers86,1244
Non-polymers3,12715
Water9,620534
1
A: Phenazine biosynthesis protein A/B
B: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5799
Polymers43,0622
Non-polymers1,5177
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-11 kcal/mol
Surface area13570 Å2
MethodPISA
2
C: Phenazine biosynthesis protein A/B
D: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,67110
Polymers43,0622
Non-polymers1,6098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-11 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.363, 69.088, 82.993
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phenazine biosynthesis protein A/B


Mass: 21531.025 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia lata (bacteria) / Gene: Bcep18194_B1568 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q396C9
#2: Chemical
ChemComp-A1IAG / (3-bromophenyl)-[2-(4-hydroxyphenyl)-6-oxidanyl-1-benzothiophen-3-yl]methanone / (3-Bromophenyl)[6-hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophen-3-yl]methanone


Mass: 425.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H13BrO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15% (w/v) PEG monomethyl ether, 0.1 M MES pH 6.14, 0.122 M ammonium acetate, 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.6→82.99 Å / Num. obs: 98772 / % possible obs: 95.6 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Χ2: 0.83 / Net I/σ(I): 11.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4561 / CC1/2: 0.806 / Rpim(I) all: 0.419 / Rrim(I) all: 1.057 / % possible all: 88.5

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Processing

Software
NameVersionClassification
XDSJan 10, 2022data reduction
Aimlessv0.7.7data scaling
PHASERv2.8.3phasing
PHENIXv1.20.1-4487refinement
autoPROCv1.0.5 (20211020)data processing
PDB_EXTRACTv4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.95 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1872 4808 4.87 %
Rwork0.1641 --
obs0.1652 98628 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.377 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5076 0 194 534 5804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095691
X-RAY DIFFRACTIONf_angle_d1.0667741
X-RAY DIFFRACTIONf_dihedral_angle_d18.0052046
X-RAY DIFFRACTIONf_chiral_restr0.061712
X-RAY DIFFRACTIONf_plane_restr0.011019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.26591240.24972944X-RAY DIFFRACTION90
1.62-1.640.25481770.24242819X-RAY DIFFRACTION87
1.64-1.660.24631670.22563166X-RAY DIFFRACTION96
1.66-1.680.24361590.21783064X-RAY DIFFRACTION96
1.68-1.70.23021740.20563086X-RAY DIFFRACTION96
1.7-1.720.20121660.19073179X-RAY DIFFRACTION96
1.72-1.750.2481520.18463122X-RAY DIFFRACTION96
1.75-1.780.20561980.18083159X-RAY DIFFRACTION96
1.78-1.80.1941380.17953145X-RAY DIFFRACTION96
1.8-1.830.22652070.17853141X-RAY DIFFRACTION97
1.83-1.860.20261560.17243131X-RAY DIFFRACTION96
1.86-1.90.17371790.1733080X-RAY DIFFRACTION96
1.9-1.930.19791650.17793185X-RAY DIFFRACTION97
1.93-1.970.21471190.17363213X-RAY DIFFRACTION96
1.97-2.020.21781290.16213140X-RAY DIFFRACTION97
2.02-2.060.22311400.1663190X-RAY DIFFRACTION96
2.06-2.120.17481670.16053132X-RAY DIFFRACTION96
2.12-2.170.23131640.16243132X-RAY DIFFRACTION95
2.17-2.240.18851340.16052814X-RAY DIFFRACTION86
2.24-2.310.20231690.163118X-RAY DIFFRACTION94
2.31-2.390.20211650.15173155X-RAY DIFFRACTION98
2.39-2.490.15461650.15253177X-RAY DIFFRACTION98
2.49-2.60.2031860.15573195X-RAY DIFFRACTION98
2.6-2.740.17051860.1513217X-RAY DIFFRACTION98
2.74-2.910.19361490.15313244X-RAY DIFFRACTION98
2.91-3.130.20131470.1623233X-RAY DIFFRACTION98
3.13-3.450.1751720.15783225X-RAY DIFFRACTION97
3.45-3.950.16691590.14593111X-RAY DIFFRACTION95
3.95-4.970.1251280.13323051X-RAY DIFFRACTION90
4.97-48.950.20021670.2073252X-RAY DIFFRACTION96
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)
16.75163.12772.53546.030.64443.89310.0622-0.09780.14330.0387-0.0050.4539-0.1495-1.3809-0.01070.24160.06010.02770.54140.01870.18118.2595-10.208212.7954
26.58733.5547-1.25773.6317-3.20754.01710.2513-0.65350.27740.2667-0.533-0.1126-0.54040.0160.23950.2823-0.00730.01310.3051-0.03330.203631.4562-5.114122.1567
38.02331.2326-5.2531.1088-0.98987.3375-0.2956-0.4645-0.68210.1043-0.0322-0.09710.58510.28270.41850.23990.02220.00140.18960.05950.262637.24-19.228414.1101
44.8585.8031-2.76197.0389-2.71942.99980.0407-0.6937-0.56140.4873-0.3059-0.58550.0570.07890.27460.24970.0082-0.02620.36370.07610.287138.7907-11.460423.8749
54.20841.2261.48071.1350.78672.784-0.0216-0.12580.1770.0601-0.0614-0.0094-0.2624-0.26140.10370.18010.03460.00990.12350.00080.153930.5216-6.59558.2509
67.34461.59840.79110.5630.53612.1861-0.0016-0.16470.11850.061-0.0172-0.0122-0.15340.1120.04140.19070.0217-0.01010.1016-0.01210.169540.7611-7.524111.5035
79.5578-0.9449-7.92181.52570.75048.0669-0.1833-0.5282-0.10630.1245-0.00950.13280.30360.10360.21080.1761-0.00580.00330.19770.02060.169828.6156-16.469913.4238
82.87723.82743.51955.10854.67534.4546-0.0658-0.0475-0.0125-0.14480.1273-0.0812-0.26240.2546-0.00390.2091-0.0149-0.01040.19350.00970.198447.7923-8.11444.8405
90.8589-0.9197-1.12145.31494.60654.11390.21330.2279-0.0258-0.59180.1654-0.2865-0.40390.7831-0.21250.2513-0.0520.05520.3386-0.01040.288653.1338-10.469-8.8445
102.5597-3.7173-0.89535.59371.11944.3647-0.18510.1365-0.36360.0994-0.06540.5419-0.1194-0.84720.23270.1919-0.0378-0.02260.4207-0.05310.232117.094-14.8222-10.269
118.6722-4.741.84269.169-4.14796.98920.16670.5615-0.4747-0.4931-0.2625-0.27550.3822-0.06090.09770.211-0.0361-0.0020.3597-0.08310.214831.1665-19.9887-20.6619
127.5327-1.81464.83791.7663-1.93477.6659-0.23240.43550.62480.0281-0.1267-0.2534-0.54510.18660.44740.2247-0.0207-0.00030.21420.05860.236437.4335-6.8085-12.1274
135.2373-5.5710.21766.0085-0.16084.2242-0.01310.1578-0.09-0.2846-0.1246-0.3962-0.2718-0.09630.15260.2388-0.00140.01270.36520.02020.302838.5708-13.9592-21.8435
143.5607-1.1982-2.10581.35390.9272.6004-0.11720.2058-0.146-0.0107-0.04250.01020.1323-0.28270.18440.1789-0.032-0.010.1632-0.02360.186230.0974-18.8874-5.995
154.797-0.5879-1.33840.0462-0.03272.1321-0.04150.1961-0.2623-0.0731-0.0756-0.03210.0701-0.00240.13580.1952-0.0250.00880.1313-0.02540.205539.9584-18.6849-8.9691
163.04420.78065.12922.42810.60128.8936-0.13820.14670.1321-0.1207-0.03980.0768-0.4709-0.48480.19420.17890.01840.01070.27620.02780.179928.6336-9.0779-11.0929
178.1557-3.4962-3.47573.86223.62093.3959-0.2586-0.1671-0.34780.20110.15960.00610.31490.10210.05360.20990.0020.01050.14970.02410.213347.4428-18.6202-2.7571
180.03160.3790.36953.4673.54483.59590.0588-0.16990.05740.28870.0464-0.0743-0.03830.65630.08920.20330.0447-0.04740.3335-0.01830.237953.145-16.7311.1625
198.41716.35381.6047.62631.40463.8358-0.11740.25740.41870.0138-0.02160.70890.1519-0.85060.1540.20.00140.03330.3763-0.0160.2065-18.2497-11.691653.5668
205.71241.13590.20053.0073-3.82325.5241-0.0196-0.36620.24020.1534-0.1836-0.2845-0.427-0.190.14320.25670.0110.00730.2351-0.02950.1824-3.9344-5.615863.4947
211.91811.86441.75233.8120.60772.21790.0139-0.4334-0.49810.36-0.25370.0220.2413-0.0520.48390.2302-0.00870.01060.22820.08210.2119-3.8362-19.009160.4674
228.41650.7489-6.20631.3547-1.22829.9223-0.3111-0.1049-0.56540.0056-0.0979-0.19950.82380.57420.47020.2550.0493-0.0070.19070.01580.26246.6098-19.616653.1113
235.49875.9743-4.64146.5347-4.81225.8888-0.0192-0.4768-0.47090.2063-0.371-0.80440.20580.17850.3940.23450.0095-0.01160.3060.03650.32754.6494-11.280465.6172
242.931.11561.65981.48381.08322.6822-0.0372-0.03420.09720.0326-0.02490.0242-0.1256-0.18180.08680.1720.02420.02870.145-0.00150.1621-4.4407-6.979349.4074
255.12231.4550.7490.54440.18652.29060.0393-0.14340.10420.095-0.0253-0.0402-0.08510.15290.00150.210.0150.0010.132-0.01740.20545.5538-7.837552.9052
267.7741-0.1625-3.91061.31860.35276.353-0.0968-0.3544-0.17860.1635-0.04470.02880.4895-0.09170.08710.2081-0.028-0.00230.19890.02690.1731-6.0776-17.028854.8511
276.42642.25962.21312.54862.40723.93670.0075-0.15480.0813-0.06760.0172-0.009-0.1042-0.0411-0.04510.191-0.00840.00530.17370.01080.192412.6982-7.551746.3793
280.3531-0.932-1.06732.32572.70893.14370.04970.2493-0.0897-0.28170.0375-0.0404-0.2550.6473-0.02330.196-0.05760.02760.3006-0.0250.242918.3729-9.64832.6077
291.868-1.8413-0.34752.54280.18520.6918-0.05320.0708-0.31680.05990.05390.56430.2258-1.111800.225-0.07-0.00880.5820.04140.2849-17.802-16.941630.8543
306.7559-2.627-0.06178.9745-4.59087.25460.04920.4372-0.2196-0.1469-0.3231-0.42590.4687-0.08320.19760.194-0.0239-0.01770.2347-0.04950.1701-3.1614-21.296521.5432
318.5401-0.78895.18611.33490.03095.9917-0.34210.59860.7032-0.0864-0.0439-0.1231-0.57630.43820.45950.2141-0.0252-0.00390.21480.07430.22272.2726-7.11629.2712
324.7892-5.01421.39795.3188-1.04114.38970.08070.55540.3685-0.3902-0.342-0.6863-0.16820.13830.23370.2579-0.04220.03840.36330.09960.33434.5975-14.708519.6669
332.699-0.5277-1.12150.81210.42542.1784-0.07690.0797-0.1153-0.00020.0119-0.03390.2167-0.29280.06880.1884-0.0354-0.00950.1670.0010.1786-4.116-19.736435.517
342.7747-0.26310.22830.5620.45411.3591-0.01560.0517-0.0464-0.07080.0243-0.06030.0354-0.0292-0.00130.1853-0.01570.01010.1470.01860.17964.0306-16.090133.4286
350.6302-1.3291-1.30454.92724.43013.9770.0909-0.4572-0.01210.61960.2215-0.19020.33560.7167-0.110.2614-0.0165-0.05840.4377-0.01510.275618.2619-15.599853.1733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 80 )
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 131 )
7X-RAY DIFFRACTION7chain 'A' and (resid 132 through 141 )
8X-RAY DIFFRACTION8chain 'A' and (resid 142 through 151 )
9X-RAY DIFFRACTION9chain 'A' and (resid 152 through 165 )
10X-RAY DIFFRACTION10chain 'B' and (resid 10 through 32 )
11X-RAY DIFFRACTION11chain 'B' and (resid 33 through 44 )
12X-RAY DIFFRACTION12chain 'B' and (resid 45 through 66 )
13X-RAY DIFFRACTION13chain 'B' and (resid 67 through 80 )
14X-RAY DIFFRACTION14chain 'B' and (resid 81 through 110 )
15X-RAY DIFFRACTION15chain 'B' and (resid 111 through 131 )
16X-RAY DIFFRACTION16chain 'B' and (resid 132 through 141 )
17X-RAY DIFFRACTION17chain 'B' and (resid 142 through 151 )
18X-RAY DIFFRACTION18chain 'B' and (resid 152 through 165 )
19X-RAY DIFFRACTION19chain 'C' and (resid 10 through 31 )
20X-RAY DIFFRACTION20chain 'C' and (resid 32 through 44 )
21X-RAY DIFFRACTION21chain 'C' and (resid 45 through 53 )
22X-RAY DIFFRACTION22chain 'C' and (resid 54 through 66 )
23X-RAY DIFFRACTION23chain 'C' and (resid 67 through 80 )
24X-RAY DIFFRACTION24chain 'C' and (resid 81 through 110 )
25X-RAY DIFFRACTION25chain 'C' and (resid 111 through 131 )
26X-RAY DIFFRACTION26chain 'C' and (resid 132 through 141 )
27X-RAY DIFFRACTION27chain 'C' and (resid 142 through 151 )
28X-RAY DIFFRACTION28chain 'C' and (resid 152 through 165 )
29X-RAY DIFFRACTION29chain 'D' and (resid 12 through 31 )
30X-RAY DIFFRACTION30chain 'D' and (resid 32 through 44 )
31X-RAY DIFFRACTION31chain 'D' and (resid 45 through 66 )
32X-RAY DIFFRACTION32chain 'D' and (resid 67 through 80 )
33X-RAY DIFFRACTION33chain 'D' and (resid 81 through 110 )
34X-RAY DIFFRACTION34chain 'D' and (resid 111 through 151 )
35X-RAY DIFFRACTION35chain 'D' and (resid 152 through 165 )

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  • 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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