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- PDB-4h3l: mPlum-E16P -

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Open data


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Basic information

Entry
Database: PDB / ID: 4h3l
TitlemPlum-E16P
ComponentsFluorescent protein plum
KeywordsFLUORESCENT PROTEIN
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fluorescent protein plum
Similarity search - Component
Biological speciesDiscosoma sp. LW-2004 (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMoore, M.M. / Chica, R.A.
CitationJournal: Plos One / Year: 2012
Title: Recovery of Red Fluorescent Protein Chromophore Maturation Deficiency through Rational Design.
Authors: Moore, M.M. / Oteng-Pabi, S.K. / Pandelieva, A.T. / Mayo, S.L. / Chica, R.A.
History
DepositionSep 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_polymer_linkage / software
Item: _software.name
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein plum
B: Fluorescent protein plum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0553
Polymers53,0322
Non-polymers231
Water7,350408
1
A: Fluorescent protein plum
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5392
Polymers26,5161
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fluorescent protein plum


Theoretical massNumber of molelcules
Total (without water)26,5161
Polymers26,5161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.229, 76.888, 95.801
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 Fluorescent protein plum / mPlum-E16P


Mass: 26515.896 Da / Num. of mol.: 2 / Mutation: E16P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. LW-2004 (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S3G7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMET66, TYR67, AND GLY68 CIRCULARIZED INTO ONE CHROMOPHORE (NRQ).

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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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.3 uL + 0.3 uL drops, precipitant: 200 mM magnesium chloride, 100 mM sodium cacodylate, pH 6.5, 50% (v/v) PEG200, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.5418, 1.5621, 1.7321
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.56211
31.73211
ReflectionResolution: 1.65→37.73 Å / Num. all: 55128 / Num. obs: 53773 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.2
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 1.7 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.3_928)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QLG
Resolution: 1.65→33.87 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 2726 5.08 %RANDOM
Rwork0.1904 ---
obs0.1923 53662 97.36 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.47 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6601 Å2-0 Å20 Å2
2---2.3107 Å2-0 Å2
3---5.9362 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 1 408 3755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123592
X-RAY DIFFRACTIONf_angle_d1.444884
X-RAY DIFFRACTIONf_dihedral_angle_d13.2411357
X-RAY DIFFRACTIONf_chiral_restr0.086504
X-RAY DIFFRACTIONf_plane_restr0.008643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.38451500.3252635X-RAY DIFFRACTION97
1.68-1.71230.37641620.3082615X-RAY DIFFRACTION97
1.7123-1.74730.3481450.2882609X-RAY DIFFRACTION96
1.7473-1.78530.35111200.2752649X-RAY DIFFRACTION96
1.7853-1.82680.2711470.23622650X-RAY DIFFRACTION98
1.8268-1.87250.29881520.22282672X-RAY DIFFRACTION98
1.8725-1.92310.23621300.20212693X-RAY DIFFRACTION98
1.9231-1.97970.22481460.19462641X-RAY DIFFRACTION98
1.9797-2.04360.2321490.18442675X-RAY DIFFRACTION97
2.0436-2.11660.23121530.18892608X-RAY DIFFRACTION96
2.1166-2.20130.22391390.18132661X-RAY DIFFRACTION97
2.2013-2.30150.25671520.17392687X-RAY DIFFRACTION98
2.3015-2.42280.1991340.16892711X-RAY DIFFRACTION98
2.4228-2.57450.24341360.16942715X-RAY DIFFRACTION98
2.5745-2.77320.19331280.17412651X-RAY DIFFRACTION95
2.7732-3.05220.20131510.1782714X-RAY DIFFRACTION98
3.0522-3.49340.2141460.18282731X-RAY DIFFRACTION98
3.4934-4.39980.18521200.15392743X-RAY DIFFRACTION96
4.3998-33.87670.20531660.20472876X-RAY DIFFRACTION98
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)
10.1473-0.0155-0.07530.04630.02120.05970.020.0191-0.0127-0.0279-0.0118-0.0415-0.0228-0.02720.04210.17230.03670.07640.1835-0.07460.3249-7.9397-24.5962-6.0625
20.22450.0116-0.08860.0088-0.03550.15160.07490.1589-0.1887-0.02940.0854-0.11540.2525-0.06340.00250.1271-0.0073-0.01930.1017-0.01160.2026-11.266-25.67378.2078
30.10010.25620.23560.66630.5670.69190.0812-0.0263-0.2123-0.03120.14970.0010.02930.08330.04660.2499-0.0126-0.06880.15290.06110.2052-8.5805-20.410627.3351
40.3847-0.03690.12310.19350.10620.30120.0790.1377-0.15410.04790.0062-0.04260.05810.05980.03010.1052-0.0115-0.00970.10750.00290.1351-14.1699-19.081112.9087
50.0355-0.016-0.0710.00720.03180.1417-0.01950.0345-0.02970.0602-0.04920.0014-0.09890.0212-0.09840.0674-0.026-0.01250.0776-0.02740.0874-7.9084-14.94810.6488
60.05640.00010.02470.02160.03330.0614-0.08960.196-0.09830.0553-0.0213-0.0073-0.0629-0.054900.13970.0008-0.0080.1232-0.03360.16380.2391-16.9301-1.8676
70.28360.0327-0.15890.46010.09090.11840.1031-0.0926-0.13430.01040.0033-0.2130.03970.01620.03930.09460.0193-0.02610.068-0.00970.1319-2.2779-12.906617.1678
80.216-0.0268-0.25640.00330.03120.3052-0.09460.0111-0.2628-0.06190.0965-0.0489-0.03270.0632-0.01160.19640.0138-0.07540.1047-0.03370.3162-6.0944-26.84048.0852
90.0088-0.0199-0.01120.08590.04210.0210.0765-0.11-0.07130.01270.0792-0.15280.04330.02210.00210.1789-0.0032-0.01590.20320.00080.1149-6.467-10.896428.5689
100.06910.02770.03230.06490.05880.05460.0227-0.14240.1444-0.01220.13570.0792-0.0334-0.05710.0080.18440.05070.01840.22130.00320.1308-16.8585-6.823828.0686
110.00790.00450.00980.00550.00880.0156-0.0114-0.1763-0.0572-0.13040.0486-0.0707-0.0915-0.12390.00030.17880.01230.01850.18270.0010.1503-17.3033-4.976815.2601
120.01390.0163-0.01160.03370.00990.0777-0.12260.14050.01360.29910.0401-0.14540.0590.0708-0.00010.1414-0.0067-0.0440.11110.00210.19752.0255-5.57466.0966
130.04290.0327-0.01730.0243-0.01280.006-0.00030.04360.20680.11150.1113-0.1030.0771-0.02970.00010.14580.01570.02070.153-0.00630.1473-8.25-3.227513.3744
140.1501-0.00010.06980.0389-0.040.073-0.1079-0.17130.0896-0.0225-0.2850.0965-0.0626-0.1269-0.00740.23730.03130.04740.1708-0.02890.2508-17.13040.518621.0695
150.0003-0.00220.00330.0143-0.02150.03160.12860.04020.07680.05610.0029-0.09050.05650.0807-00.15810.00860.00970.1448-0.01640.1528-0.2605-7.846112.8973
160.0063-0.0017-0.00040.0040.0030.0023-0.1497-0.0715-0.0428-0.0403-0.03810.1010.06720.0166-0.00020.12190.0131-0.00060.188-0.02090.19067.3481-20.89714.9144
170.0307-0.01740.03740.0097-0.0210.04430.05360.0587-0.0229-0.03490.04110.0452-0.0730.0158-00.12140.0048-0.00980.1353-0.00270.15210.6987-8.8554-0.0688
180.3479-0.3056-0.18351.2373-0.33920.3550.03030.02750.1246-0.1579-0.1201-0.07620.0885-0.0399-0.07010.0821-0.0007-0.00640.1712-0.02420.0833-21.053-12.631311.6963
190.011-0.00530.00080.014-0.00770.0045-0.01240.0262-0.074-0.0062-0.11860.1628-0.0171-0.1931-0.00010.154-0.03670.02540.1595-0.00220.1767-22.2038-18.986818.3435
200.008-0.0145-0.00180.02740.00760.01410.00030.0345-0.05180.0404-0.0134-0.0454-0.0654-0.104500.12710.00460.00650.12520.00930.1615-9.9928-7.34930.1827
210.00610.0199-0.00220.23180.05270.02280.04650.0059-0.06990.0693-0.09220.05740.10340.33840.00050.1369-0.0244-0.0290.17480.06230.156411.5487-24.995953.089
220.1859-0.0384-0.01310.05040.00940.07340.02440.0278-0.1037-0.07230.12490.16410.0678-0.1055-0.04130.1245-0.0035-0.03520.10220.02930.099111.3687-23.530433.5033
230.3843-0.2449-0.31830.4035-0.05520.53250.0730.0677-0.09110.0090.0893-0.00370.05520.00930.14230.1389-0.0203-0.0740.1375-0.06650.228711.707-22.230820.264
240.05650.0139-0.03140.0023-0.00390.18250.0376-0.0983-0.14790.0089-0.0159-0.0190.10670.02460.02710.11770.007-0.00620.13950.00790.078717.1533-22.202739.1771
250.0535-0.02460.0210.0613-0.05040.0408-0.0652-0.04660.00670.05240.05170.0643-0.05440.2027-00.1466-0.0066-0.0150.17050.03440.148414.7738-14.996729.844
260.0466-0.06520.01730.0923-0.02340.0069-0.0292-0.0461-0.1288-0.0938-0.1510.0423-0.04940.0267-0.01290.0950.0136-0.01250.13040.00330.09469.3897-14.530448.2099
270.04340.017-0.02870.0184-0.00820.0732-0.0151-0.1011-0.0278-0.02960.0730.0373-0.094-0.01490.0040.12670.00160.00310.12080.02990.13141.2022-17.642650.1929
280.1913-0.0132-0.15290.3751-0.27510.5960.05440.09510.067-0.04360.04480.0558-0.0863-0.05780.55630.0806-0.0262-0.02840.04160.07370.03714.1164-13.908231.8636
290.00620.00370.01140.00180.00620.0187-0.02290.122-0.2216-0.01490.0953-0.01530.06290.0366-00.1551-0.0024-0.03090.1180.00440.17177.7121-26.453138.4693
300.0305-0.0444-0.01880.06420.02770.012-0.07990.1680.0262-0.01570.14520.13450.08370.05910.00470.1667-0.0273-0.0150.23420.07440.12210.885-8.515318.1627
310.0548-0.0303-0.04360.01660.0240.03450.04550.120.07330.00460.03580.0356-0.1465-0.01140.02520.1518-0.06520.01460.26850.07650.11319.7327-8.350220.5775
320.46770.01910.26240.01570.01990.1528-0.07830.0714-0.01170.07140.04180.029-0.09930.105-0.03090.1893-0.08610.01370.15050.05240.160919.8751-4.482732.53
330.0055-0.01610.00760.0552-0.03150.019-0.13-0.01630.0889-0.1120.13170.0801-0.015-0.0727-00.16240.00390.00140.11280.02120.17380.4381-5.732341.9419
340.0026-0.00290.00210.003-0.00240.0018-0.05940.00370.0662-0.0756-0.0827-0.0209-0.0703-0.0514-0.00040.11530.00170.02250.10730.00690.2278-0.3758-5.855239.4364
350.2270.10490.03410.1533-0.18180.37740.00410.06340.13880.2593-0.00810.0149-0.0313-0.0211-0.10540.1624-0.02130.02820.12410.09680.198415.1444-2.143331.9711
360.03360.13520.14240.5480.57550.6052-0.0817-0.01480.111-0.055-0.1272-0.2019-0.14450.2204-0.44510.2053-0.0655-0.01280.18570.08930.187815.6323-0.253528.3341
370.0066-0.0073-0.00380.01220.01060.01170.02750.0653-0.00430.031-0.10390.04790.1806-0.117600.133-0.02430.00790.16950.03470.1437-0.7865-11.848737.8493
380.0864-0.01060.09640.00220.00350.1665-0.02990.08680.02250.0380.02180.05820.00820.0068-0.00010.1148-0.00530.02560.13330.02580.12558.758-12.451442.7443
390.28610.0648-0.00560.1630.04050.0117-0.07390.03570.0098-0.0012-0.0849-0.0304-0.10230.169-0.05260.15740.02070.0140.21680.02590.071623.8024-19.251429.4636
400.40430.06510.27880.12660.17190.33250.03420.23760.12410.01770.03490.0644-0.1184-0.03930.04580.16770.0150.02240.1070.03830.144212.0268-7.442647.8127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 6:10)
2X-RAY DIFFRACTION2(chain A and resid 11:18)
3X-RAY DIFFRACTION3(chain A and resid 19:28)
4X-RAY DIFFRACTION4(chain A and resid 29:69)
5X-RAY DIFFRACTION5(chain A and resid 70:74)
6X-RAY DIFFRACTION6(chain A and resid 75:91)
7X-RAY DIFFRACTION7(chain A and resid 92:113)
8X-RAY DIFFRACTION8(chain A and resid 114:123)
9X-RAY DIFFRACTION9(chain A and resid 124:131)
10X-RAY DIFFRACTION10(chain A and resid 132:140)
11X-RAY DIFFRACTION11(chain A and resid 141:144)
12X-RAY DIFFRACTION12(chain A and resid 145:156)
13X-RAY DIFFRACTION13(chain A and resid 157:167)
14X-RAY DIFFRACTION14(chain A and resid 168:174)
15X-RAY DIFFRACTION15(chain A and resid 175:181)
16X-RAY DIFFRACTION16(chain A and resid 182:185)
17X-RAY DIFFRACTION17(chain A and resid 186:197)
18X-RAY DIFFRACTION18(chain A and resid 198:204)
19X-RAY DIFFRACTION19(chain A and resid 205:213)
20X-RAY DIFFRACTION20(chain A and resid 214:222)
21X-RAY DIFFRACTION21(chain B and resid 6:11)
22X-RAY DIFFRACTION22(chain B and resid 12:23)
23X-RAY DIFFRACTION23(chain B and resid 24:28)
24X-RAY DIFFRACTION24(chain B and resid 29:52)
25X-RAY DIFFRACTION25(chain B and resid 53:69)
26X-RAY DIFFRACTION26(chain B and resid 70:75)
27X-RAY DIFFRACTION27(chain B and resid 76:90)
28X-RAY DIFFRACTION28(chain B and resid 91:113)
29X-RAY DIFFRACTION29(chain B and resid 114:124)
30X-RAY DIFFRACTION30(chain B and resid 125:134)
31X-RAY DIFFRACTION31(chain B and resid 135:140)
32X-RAY DIFFRACTION32(chain B and resid 141:144)
33X-RAY DIFFRACTION33(chain B and resid 145:156)
34X-RAY DIFFRACTION34(chain B and resid 157:160)
35X-RAY DIFFRACTION35(chain B and resid 161:167)
36X-RAY DIFFRACTION36(chain B and resid 168:177)
37X-RAY DIFFRACTION37(chain B and resid 178:182)
38X-RAY DIFFRACTION38(chain B and resid 183:205)
39X-RAY DIFFRACTION39(chain B and resid 206:213)
40X-RAY DIFFRACTION40(chain B and resid 214:222)

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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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