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- PDB-6uba: Crystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase... -

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Basic information

Entry
Database: PDB / ID: 6uba
TitleCrystal structure of a GH128 (subgroup VI) exo-beta-1,3-glucanase from Aureobasidium namibiae (AnGH128_VI) in complex with laminaritriose
ComponentsGlyco_hydro_cc domain-containing protein
KeywordsHYDROLASE / Glycosyl hydrolase / CARBOHYDRATE
Function / homologyfungal-type cell wall polysaccharide metabolic process / : / Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / fungal-type cell wall / Glycoside hydrolase superfamily / beta-laminaribiose / Asl1-like glycosyl hydrolase catalytic domain-containing protein
Function and homology information
Biological speciesAureobasidium namibiae CBS 147.97 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSantos, C.R. / Vieira, P.S. / Domingues, M.N. / Cordeiro, R.L. / Tomazini, A. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15/26982-0 Brazil
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural insights into beta-1,3-glucan cleavage by a glycoside hydrolase family.
Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. ...Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. / Junior, A.T. / Souza, B.P. / Prates, E.T. / Gozzo, F.C. / Persinoti, G.F. / Skaf, M.S. / Murakami, M.T.
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glyco_hydro_cc domain-containing protein
B: Glyco_hydro_cc domain-containing protein
C: Glyco_hydro_cc domain-containing protein
D: Glyco_hydro_cc domain-containing protein
E: Glyco_hydro_cc domain-containing protein
F: Glyco_hydro_cc domain-containing protein
G: Glyco_hydro_cc domain-containing protein
H: Glyco_hydro_cc domain-containing protein
I: Glyco_hydro_cc domain-containing protein
J: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,41630
Polymers308,11110
Non-polymers8,30520
Water12,592699
1
A: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6583
Polymers30,8111
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6583
Polymers30,8111
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6583
Polymers30,8111
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6583
Polymers30,8111
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4963
Polymers30,8111
Non-polymers6852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6583
Polymers30,8111
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6583
Polymers30,8111
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6583
Polymers30,8111
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6583
Polymers30,8111
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6583
Polymers30,8111
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.262, 152.798, 169.423
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110B
210C
111B
211D
112B
212E
113B
213F
114B
214G
115B
215H
116B
216I
117B
217J
118C
218D
119C
219E
120C
220F
121C
221G
122C
222H
123C
223I
124C
224J
125D
225E
126D
226F
127D
227G
128D
228H
129D
229I
130D
230J
131E
231F
132E
232G
133E
233H
134E
234I
135E
235J
136F
236G
137F
237H
138F
238I
139F
239J
140G
240H
141G
241I
142G
242J
143H
243I
144H
244J
145I
245J

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEAA0 - 24620 - 266
21ILEILEBB0 - 24620 - 266
12ILEILEAA0 - 24620 - 266
22ILEILECC0 - 24620 - 266
13ILEILEAA0 - 24620 - 266
23ILEILEDD0 - 24620 - 266
14HISHISAA0 - 24520 - 265
24HISHISEE0 - 24520 - 265
15ILEILEAA0 - 24620 - 266
25ILEILEFF0 - 24620 - 266
16ILEILEAA0 - 24620 - 266
26ILEILEGG0 - 24620 - 266
17ILEILEAA0 - 24620 - 266
27ILEILEHH0 - 24620 - 266
18ILEILEAA0 - 24620 - 266
28ILEILEII0 - 24620 - 266
19ILEILEAA0 - 24620 - 266
29ILEILEJJ0 - 24620 - 266
110ILEILEBB0 - 24620 - 266
210ILEILECC0 - 24620 - 266
111ILEILEBB0 - 24620 - 266
211ILEILEDD0 - 24620 - 266
112HISHISBB0 - 24520 - 265
212HISHISEE0 - 24520 - 265
113ILEILEBB0 - 24620 - 266
213ILEILEFF0 - 24620 - 266
114ILEILEBB0 - 24620 - 266
214ILEILEGG0 - 24620 - 266
115ILEILEBB0 - 24620 - 266
215ILEILEHH0 - 24620 - 266
116ILEILEBB0 - 24620 - 266
216ILEILEII0 - 24620 - 266
117ILEILEBB0 - 24620 - 266
217ILEILEJJ0 - 24620 - 266
118ILEILECC0 - 24620 - 266
218ILEILEDD0 - 24620 - 266
119HISHISCC0 - 24520 - 265
219HISHISEE0 - 24520 - 265
120ILEILECC0 - 24620 - 266
220ILEILEFF0 - 24620 - 266
121ILEILECC0 - 24620 - 266
221ILEILEGG0 - 24620 - 266
122ILEILECC0 - 24620 - 266
222ILEILEHH0 - 24620 - 266
123ILEILECC0 - 24620 - 266
223ILEILEII0 - 24620 - 266
124ILEILECC0 - 24620 - 266
224ILEILEJJ0 - 24620 - 266
125HISHISDD0 - 24520 - 265
225HISHISEE0 - 24520 - 265
126ILEILEDD0 - 24620 - 266
226ILEILEFF0 - 24620 - 266
127ILEILEDD0 - 24620 - 266
227ILEILEGG0 - 24620 - 266
128ILEILEDD0 - 24620 - 266
228ILEILEHH0 - 24620 - 266
129ILEILEDD0 - 24620 - 266
229ILEILEII0 - 24620 - 266
130ILEILEDD0 - 24620 - 266
230ILEILEJJ0 - 24620 - 266
131HISHISEE0 - 24520 - 265
231HISHISFF0 - 24520 - 265
132HISHISEE0 - 24520 - 265
232HISHISGG0 - 24520 - 265
133HISHISEE0 - 24520 - 265
233HISHISHH0 - 24520 - 265
134HISHISEE0 - 24520 - 265
234HISHISII0 - 24520 - 265
135HISHISEE0 - 24520 - 265
235HISHISJJ0 - 24520 - 265
136ILEILEFF0 - 24620 - 266
236ILEILEGG0 - 24620 - 266
137ILEILEFF0 - 24620 - 266
237ILEILEHH0 - 24620 - 266
138ILEILEFF0 - 24620 - 266
238ILEILEII0 - 24620 - 266
139ILEILEFF0 - 24620 - 266
239ILEILEJJ0 - 24620 - 266
140ILEILEGG0 - 24620 - 266
240ILEILEHH0 - 24620 - 266
141ILEILEGG0 - 24620 - 266
241ILEILEII0 - 24620 - 266
142ILEILEGG0 - 24620 - 266
242ILEILEJJ0 - 24620 - 266
143ILEILEHH0 - 24620 - 266
243ILEILEII0 - 24620 - 266
144ILEILEHH0 - 24620 - 266
244ILEILEJJ0 - 24620 - 266
145ILEILEII0 - 24620 - 266
245ILEILEJJ0 - 24620 - 266

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

#1: Protein
Glyco_hydro_cc domain-containing protein


Mass: 30811.098 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aureobasidium namibiae CBS 147.97 (fungus)
Gene: M436DRAFT_66913 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A074W9U7
#2: Polysaccharide
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.18 M tri-ammonium citrate, 18% v/v PEG 3350, 0.01 M Cobalt (II) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45857 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45857 Å / Relative weight: 1
ReflectionResolution: 2.4→49.35 Å / Num. obs: 123227 / % possible obs: 99 % / Redundancy: 11.9 % / CC1/2: 0.99 / Net I/σ(I): 6.24
Reflection shellResolution: 2.4→2.54 Å / Mean I/σ(I) obs: 1.15 / Num. unique obs: 19656 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UB8

6ub8


Resolution: 2.4→49.35 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.299 / SU ML: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.484 / ESU R Free: 0.268
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 6161 5 %RANDOM
Rwork0.2367 ---
obs0.2377 117052 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.31 Å2 / Biso mean: 35.357 Å2 / Biso min: 11.53 Å2
Baniso -1Baniso -2Baniso -3
1-6.36 Å20 Å2-0 Å2
2---4.52 Å20 Å2
3----1.84 Å2
Refinement stepCycle: final / Resolution: 2.4→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20305 0 559 699 21563
Biso mean--48.42 28.3 -
Num. residues----2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01321580
X-RAY DIFFRACTIONr_bond_other_d0.0010.01719128
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.67729410
X-RAY DIFFRACTIONr_angle_other_deg1.111.61144598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8325.2762659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17222.7271100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00515.1993688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.08615100
X-RAY DIFFRACTIONr_chiral_restr0.0510.22827
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0223231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024493
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A86550.04
12B86550.04
21A86450.04
22C86450.04
31A86240.04
32D86240.04
41A86130.04
42E86130.04
51A86530.04
52F86530.04
61A86250.04
62G86250.04
71A86300.04
72H86300.04
81A86190.05
82I86190.05
91A86260.04
92J86260.04
101B86250.04
102C86250.04
111B85960.04
112D85960.04
121B85820.05
122E85820.05
131B86180.05
132F86180.05
141B86160.04
142G86160.04
151B86070.05
152H86070.05
161B86130.05
162I86130.05
171B86150.05
172J86150.05
181C85920.04
182D85920.04
191C85770.05
192E85770.05
201C86310.04
202F86310.04
211C86290.04
212G86290.04
221C86260.04
222H86260.04
231C86110.05
232I86110.05
241C86500.04
242J86500.04
251D85650.04
252E85650.04
261D86000.04
262F86000.04
271D86050.04
272G86050.04
281D86240.04
282H86240.04
291D86170.04
292I86170.04
301D85730.05
302J85730.05
311E86130.04
312F86130.04
321E85570.05
322G85570.05
331E85710.05
332H85710.05
341E85660.05
342I85660.05
351E85620.05
352J85620.05
361F86130.04
362G86130.04
371F86150.05
372H86150.05
381F86150.04
382I86150.04
391F86200.04
392J86200.04
401G86460.04
402H86460.04
411G86420.04
412I86420.04
421G86270.04
422J86270.04
431H86770.04
432I86770.04
441H86520.05
442J86520.05
451I86120.05
452J86120.05
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 449 -
Rwork0.36 8535 -
all-8984 -
obs--99.38 %

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