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- PDB-4p56: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR... -

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Basic information

Entry
Database: PDB / ID: 4p56
TitleCRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM BORDETELLA BRONCHISEPTICA, TARGET EFI-510038 (BB2442), WITH BOUND (R)-MANDELATE and (S)-MANDELATE
ComponentsPutative extracellular solute-binding protein
KeywordsSOLUTE-BINDING PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics
Function / homology
Function and homology information


transmembrane transport
Similarity search - Function
Bacterial extracellular solute-binding protein, family 7 / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / (R)-MANDELIC ACID / (S)-MANDELIC ACID / Putative extracellular solute-binding protein / Putative extracellular solute-binding protein
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsVetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. ...Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hillerich, B. / Love, J. / Seidel, R.D. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM093342 United States
CitationJournal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. / Seidel, R.D. / Quinn, R.J. / Osterman, A.L. / Cronan, J.E. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C.
History
DepositionMar 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative extracellular solute-binding protein
B: Putative extracellular solute-binding protein
C: Putative extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7429
Polymers112,8333
Non-polymers9096
Water16,502916
1
A: Putative extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0634
Polymers37,6111
Non-polymers4523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7632
Polymers37,6111
Non-polymers1521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative extracellular solute-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9153
Polymers37,6111
Non-polymers3042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.402, 82.635, 80.575
Angle α, β, γ (deg.)90.000, 90.840, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative extracellular solute-binding protein / TRAP PERIPLASMIC SOLUTE BINDING PROTEIN


Mass: 37611.004 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB50 / Gene: BB2442 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WJQ1, UniProt: A0A0H3LM73*PLUS
#2: Chemical ChemComp-RMN / (R)-MANDELIC ACID


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-SMN / (S)-MANDELIC ACID


Mass: 152.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 2.2 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein (30.10 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10mM pparamandelic acid); Reservoir (0.1 M Tris pH 8.5, 30 %(w/v) PEG 1000); Cryoprotection (80% PEG1000, 20% Reservoir)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 24, 2014 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 71761 / % possible obs: 93.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.29 Å2 / Rmerge(I) obs: 0.092 / Χ2: 0.993 / Net I/av σ(I): 18.731 / Net I/σ(I): 8.7 / Num. measured all: 462324
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.935.70.84935790.81493.2
1.93-1.975.70.6535680.80292.9
1.97-2.015.80.49935520.82992.5
2.01-2.055.90.43934860.83892.1
2.05-2.095.90.36735530.85191.8
2.09-2.1460.31135040.8491.5
2.14-2.196.10.27234650.85790.7
2.19-2.256.10.23634590.88490.5
2.25-2.326.20.20734950.88890.5
2.32-2.396.30.1934280.90190.1
2.39-2.486.30.17334770.94289.9
2.48-2.586.30.14734501.00889.8
2.58-2.76.50.14234371.15989.6
2.7-2.846.50.12134921.27890.3
2.84-3.026.60.10535671.37893
3.02-3.256.70.07937451.21897.7
3.25-3.587.10.06338591.14499.4
3.58-4.097.60.05338501.1499.9
4.09-5.167.70.04438911.054100
5.16-1007.40.04139040.81198.2

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.9→26.798 Å / FOM work R set: 0.8764 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2011 3581 5.02 %
Rwork0.15 67738 -
obs0.1526 71319 92.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.94 Å2 / Biso mean: 20.47 Å2 / Biso min: 4.01 Å2
Refinement stepCycle: final / Resolution: 1.9→26.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7209 0 120 916 8245
Biso mean--29.89 28.41 -
Num. residues----947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117467
X-RAY DIFFRACTIONf_angle_d1.29410133
X-RAY DIFFRACTIONf_chiral_restr0.0751133
X-RAY DIFFRACTIONf_plane_restr0.0071314
X-RAY DIFFRACTIONf_dihedral_angle_d13.5372664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92080.22861050.1962111221674
1.9208-1.94710.26991600.19222509266991
1.9471-1.97490.24271270.18482564269191
1.9749-2.00440.24791090.18192618272792
2.0044-2.03570.24351300.17392578270892
2.0357-2.0690.22531440.16542577272191
2.069-2.10470.23561280.15982579270792
2.1047-2.1430.21821360.14972535267191
2.143-2.18420.21221330.14762578271190
2.1842-2.22870.22481240.14492545266991
2.2287-2.27720.191460.13722530267691
2.2772-2.33010.20971480.13852529267790
2.3301-2.38830.17071220.14522555267790
2.3883-2.45290.20841280.14712528265690
2.4529-2.5250.20021380.14912535267389
2.525-2.60640.20651320.14762513264590
2.6064-2.69950.19431460.15962515266189
2.6995-2.80750.23531420.15192529267190
2.8075-2.93510.23521210.16592592271391
2.9351-3.08960.19971370.162704284195
3.0896-3.28290.22521620.15632777293998
3.2829-3.53590.18881760.14972790296699
3.5359-3.89070.17681390.137628422981100
3.8907-4.45150.17111610.126228513012100
4.4515-5.60.18311410.126928572998100
5.6-26.80090.17481460.16262897304399
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)
11.1981-0.8102-0.72070.77610.47771.2954-0.09580.0563-0.37310.1094-0.03780.1990.3148-0.01540.09420.2223-0.00630.01970.0828-0.01950.12930.866637.46339.1191
21.878-0.94320.20551.5316-0.10740.83020.0034-0.0808-0.05070.17330.0107-0.06940.10710.008-0.0180.17820.0002-0.01250.0601-0.00510.070731.425942.599918.4029
31.8447-0.2746-0.25130.87730.1280.3014-0.05570.12140.1320.0719-0.0034-0.0167-0.13630.01680.05030.1776-0.0229-0.01580.0596-0.01370.100728.08858.92615.6657
42.1224-0.05930.15950.98040.13860.9342-0.12190.12790.09330.06740.04960.0811-0.0415-0.12130.06780.1196-0.0083-0.00090.0483-0.01220.065317.679456.614110.264
51.98970.8985-0.27472.4424-1.07481.6051-0.0681-0.0810.11360.2198-0.04090.1651-0.0093-0.0530.09070.14850.02490.04190.1051-0.03070.115311.363355.174615.7474
62.2134-0.4153-0.50941.34750.45861.9026-0.13810.1527-0.2572-0.070.01280.17630.138-0.29340.08630.1061-0.03120.00560.1307-0.01570.1038.961250.12337.4459
73.4422-1.4530.40511.97110.6692.213-0.0450.01120.19550.1850.1327-0.34780.11350.3603-0.10990.1331-0.0035-0.01470.0739-0.0320.146442.390644.565111.2853
86.83490.26921.17991.04120.2531.812-0.01280.5445-0.1473-0.07340.03680.05590.1243-0.15350.02880.1377-0.01610.0180.1531-0.05560.076921.939645.283-0.8482
93.1511.64781.51933.62381.58382.8845-0.28590.43930.3995-0.39870.20820.5002-0.2168-0.22640.08340.1403-0.0133-0.04620.26740.05990.21616.939761.63350.0544
104.2511.18290.92961.70740.01461.4365-0.11630.26010.3895-0.01460.04120.2394-0.07630.04830.06540.1811-0.0375-0.00550.090.00690.122429.668170.8759.8431
113.55791.42361.27343.99170.8972.7782-0.03390.3851-0.0878-0.66710.12660.2320.2867-0.1167-0.08350.3541-0.0813-0.03720.16560.03810.124629.210862.8463-4.2552
120.9594-0.24290.06120.84990.32462.4095-0.0656-0.0453-0.02490.07830.02870.17960.2578-0.32550.02690.0834-0.02560.01460.10160.01270.168121.93833.848955.3598
131.08620.0005-0.22410.85020.25261.44670.00870.02540.0923-0.08120.0089-0.0154-0.08170.2514-0.00520.0692-0.0139-0.00670.09370.02480.105737.976941.012951.867
141.074-0.4392-0.68371.0450.70192.4285-0.0673-0.07670.1265-0.00180.07520.1408-0.05320.2263-0.00720.0401-0.0063-0.00260.07710.030.125436.293141.322151.7373
151.7081-0.05410.10941.5840.32671.49430.04330.09290.0641-0.1745-0.0133-0.0635-0.04250.1921-0.03220.14470.00210.01840.14220.04880.081740.57735.094731.7964
161.172-0.19890.09981.1563-0.3782.4155-0.02430.0718-0.1844-0.1612-0.01870.01060.26210.09080.02420.13020.02460.00170.0817-0.00710.076938.731327.585536.4091
173.1302-0.9669-1.96361.69750.28143.7934-0.1015-0.25470.12540.2268-0.01380.0758-0.1002-0.06310.10120.0639-0.0163-0.00390.0746-0.04070.096224.780841.51164.5226
181.1563-0.1974-0.19631.85291.44892.70740.0275-0.0011-0.1211-0.00920.0168-0.10030.39130.0451-0.05290.15870.02940.01720.07080.03410.113237.32425.118552.2121
193.04581.5163-0.24516.2038-0.20351.6419-0.00560.0656-0.2168-0.25090.0001-0.44840.28130.53970.0090.1410.06450.0260.30980.01830.134951.950427.702835.9075
202.7918-0.3766-0.78193.82831.54155.61420.20970.10490.3601-0.0077-0.0608-0.1701-0.25580.2408-0.16150.0866-0.07490.01330.22530.0110.196849.685251.016149.6617
211.23240.47290.11811.9669-0.05680.280.0082-0.2081-0.10620.0802-0.0141-0.22460.07040.1164-0.06730.0185-0.0012-0.01340.44720.05070.187251.542836.713758.2441
221.73840.72120.39132.13040.91012.88480.0273-0.1024-0.08120.3115-0.004-0.06190.10980.232-0.01550.10660.01950.01980.1260.02370.12153.482913.487651.435
230.12020.2520.16960.65010.56951.6533-0.16680.13750.2499-0.2823-0.03580.1847-0.91940.2810.01130.3713-0.0883-0.08540.18520.07970.25451.513321.846734.6362
241.0546-0.2032-0.11371.67320.64862.04870.02130.25270.0746-0.2816-0.23310.3433-0.2041-0.22040.20410.13520.0044-0.07340.22170.00680.2119-6.74127.118322.1441
250.59090.09720.16720.96040.93032.4027-0.05160.05490.05960.0552-0.04230.0995-0.01130.1440.08560.0749-0.0195-0.00380.13120.07070.18481.911710.495338.2918
261.5463-0.27030.51931.07410.57131.00080.03880.25730.0716-0.2086-0.06340.0211-0.12720.5301-0.00560.1186-0.04940.01220.36850.10040.16758.18769.720925.6206
270.15030.2505-0.2210.6046-0.4420.5377-0.1305-0.03090.0675-0.1391-0.0418-0.0187-0.32970.16120.10250.9242-0.167-0.11450.32560.24580.40032.319829.731826.3127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 57 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 94 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 128 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 129 through 173 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 200 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 236 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 237 through 262 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 263 through 285 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 286 through 309 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 310 through 324 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 325 through 341 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 26 through 81 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 82 through 128 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 129 through 153 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 154 through 200 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 201 through 236 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 237 through 262 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 263 through 285 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 286 through 307 )B0
20X-RAY DIFFRACTION20chain 'B' and (resid 308 through 324 )B0
21X-RAY DIFFRACTION21chain 'B' and (resid 325 through 342 )B0
22X-RAY DIFFRACTION22chain 'C' and (resid 26 through 91 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 92 through 153 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 154 through 191 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 192 through 262 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 263 through 309 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 310 through 340 )C0

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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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