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- PDB-5daj: Crystal structure of NalD, the secondary repressor of MexAB-OprM ... -

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Basic information

Entry
Database: PDB / ID: 5daj
TitleCrystal structure of NalD, the secondary repressor of MexAB-OprM multidrug efflux pump in Pseudomonas aeruginosa
ComponentsNalD
KeywordsTRANSCRIPTION REGULATOR / Repressor / Transcriptional regulator / TetR family
Function / homology
Function and homology information


negative regulation of transport / negative regulation of transmembrane transport / negative regulation of transporter activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...Transcription regulator MAATS, C-terminal / MAATS-type transcriptional repressor, C-terminal region / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsChen, W.Z. / Wang, D. / Huang, S.Q. / Hu, Q.Y. / Liu, X.C. / Gan, J.H. / Chen, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Novobiocin binding to NalD induces the expression of the MexAB-OprM pump in Pseudomonas aeruginosa
Authors: Chen, W.Z. / Wang, D. / Zhou, W. / Sang, H. / Liu, X.C. / Ge, Z. / Zhang, J. / Lan, L. / Yang, C.G. / Chen, H.
History
DepositionAug 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Apr 12, 2023Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / database_2 ...citation / database_2 / pdbx_audit_support / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _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: NalD
B: NalD
C: NalD
D: NalD
E: NalD
F: NalD
G: NalD
H: NalD


Theoretical massNumber of molelcules
Total (without water)198,6848
Polymers198,6848
Non-polymers00
Water18010
1
A: NalD
B: NalD


Theoretical massNumber of molelcules
Total (without water)49,6712
Polymers49,6712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-15 kcal/mol
Surface area17300 Å2
MethodPISA
2
C: NalD
D: NalD


Theoretical massNumber of molelcules
Total (without water)49,6712
Polymers49,6712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-14 kcal/mol
Surface area17890 Å2
MethodPISA
3
E: NalD
F: NalD


Theoretical massNumber of molelcules
Total (without water)49,6712
Polymers49,6712
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-15 kcal/mol
Surface area17160 Å2
MethodPISA
4
G: NalD
H: NalD


Theoretical massNumber of molelcules
Total (without water)49,6712
Polymers49,6712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-15 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.639, 128.137, 266.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASPAA7 - 2047 - 204
21ASPASPASPASPBB7 - 2047 - 204
12LYSLYSTRPTRPAA5 - 2055 - 205
22LYSLYSTRPTRPCC5 - 2055 - 205
13ASPASPTRPTRPAA7 - 2057 - 205
23ASPASPTRPTRPDD7 - 2057 - 205
14SERSERASPASPAA8 - 2048 - 204
24SERSERASPASPEE8 - 2048 - 204
15ASPASPTRPTRPAA7 - 2057 - 205
25ASPASPTRPTRPFF7 - 2057 - 205
16SERSERTRPTRPAA8 - 2058 - 205
26SERSERTRPTRPGG8 - 2058 - 205
17GLUGLUASPASPAA6 - 2046 - 204
27GLUGLUASPASPHH6 - 2046 - 204
18ASPASPTRPTRPBB7 - 2057 - 205
28ASPASPTRPTRPCC7 - 2057 - 205
19ASPASPTRPTRPBB7 - 2057 - 205
29ASPASPTRPTRPDD7 - 2057 - 205
110SERSERTRPTRPBB8 - 2058 - 205
210SERSERTRPTRPEE8 - 2058 - 205
111ASPASPTRPTRPBB7 - 2057 - 205
211ASPASPTRPTRPFF7 - 2057 - 205
112SERSERTRPTRPBB8 - 2058 - 205
212SERSERTRPTRPGG8 - 2058 - 205
113ASPASPASPASPBB7 - 2047 - 204
213ASPASPASPASPHH7 - 2047 - 204
114ASPASPASPASPCC7 - 2047 - 204
214ASPASPASPASPDD7 - 2047 - 204
115SERSERASPASPCC8 - 2048 - 204
215SERSERASPASPEE8 - 2048 - 204
116ASPASPASPASPCC7 - 2047 - 204
216ASPASPASPASPFF7 - 2047 - 204
117SERSERTRPTRPCC8 - 2058 - 205
217SERSERTRPTRPGG8 - 2058 - 205
118GLUGLUASPASPCC6 - 2046 - 204
218GLUGLUASPASPHH6 - 2046 - 204
119SERSERTRPTRPDD8 - 2058 - 205
219SERSERTRPTRPEE8 - 2058 - 205
120ASPASPTRPTRPDD7 - 2057 - 205
220ASPASPTRPTRPFF7 - 2057 - 205
121SERSERTRPTRPDD8 - 2058 - 205
221SERSERTRPTRPGG8 - 2058 - 205
122ASPASPTRPTRPDD7 - 2057 - 205
222ASPASPTRPTRPHH7 - 2057 - 205
123SERSERTRPTRPEE8 - 2058 - 205
223SERSERTRPTRPFF8 - 2058 - 205
124SERSERTRPTRPEE8 - 2058 - 205
224SERSERTRPTRPGG8 - 2058 - 205
125SERSERASPASPEE8 - 2048 - 204
225SERSERASPASPHH8 - 2048 - 204
126SERSERTRPTRPFF8 - 2058 - 205
226SERSERTRPTRPGG8 - 2058 - 205
127ASPASPASPASPFF7 - 2047 - 204
227ASPASPASPASPHH7 - 2047 - 204
128SERSERTRPTRPGG8 - 2058 - 205
228SERSERTRPTRPHH8 - 2058 - 205

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

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Components

#1: Protein
NalD


Mass: 24835.490 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: nalD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HY46
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.36 % / Description: platelike
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Tacsimate, Sodium citrate tribasic dihydrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 61847 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rsym value: 0.1 / Net I/σ(I): 17.4
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 31.244 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2661 3122 5.1 %RANDOM
Rwork0.21048 ---
obs0.21335 58632 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.04 Å2
Baniso -1Baniso -2Baniso -3
1--4.52 Å2-0 Å20 Å2
2--2.23 Å2-0 Å2
3---2.28 Å2
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12585 0 0 10 12595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912824
X-RAY DIFFRACTIONr_bond_other_d0.0060.0212372
X-RAY DIFFRACTIONr_angle_refined_deg1.3051.97617337
X-RAY DIFFRACTIONr_angle_other_deg1.485328254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.73451544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.25723.023655
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15152159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.33715145
X-RAY DIFFRACTIONr_chiral_restr0.0690.21949
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114419
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023098
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.2866.8876221
X-RAY DIFFRACTIONr_mcbond_other7.2876.8876220
X-RAY DIFFRACTIONr_mcangle_it9.82310.3237750
X-RAY DIFFRACTIONr_mcangle_other9.82310.3237751
X-RAY DIFFRACTIONr_scbond_it7.9697.5146603
X-RAY DIFFRACTIONr_scbond_other7.9697.5146604
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.25411.0419588
X-RAY DIFFRACTIONr_long_range_B_refined11.8854.13813963
X-RAY DIFFRACTIONr_long_range_B_other11.75954.1313960
X-RAY DIFFRACTIONr_rigid_bond_restr5.832325196
X-RAY DIFFRACTIONr_sphericity_free69.05452
X-RAY DIFFRACTIONr_sphericity_bonded41.922524965
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A239540.06
12B239540.06
21A234540.07
22C234540.07
31A234140.07
32D234140.07
41A232600.07
42E232600.07
51A232820.07
52F232820.07
61A234420.07
62G234420.07
71A228700.09
72H228700.09
81B235640.07
82C235640.07
91B234500.07
92D234500.07
101B235240.07
102E235240.07
111B236120.07
112F236120.07
121B236760.07
122G236760.07
131B232540.08
132H232540.08
141C229440.07
142D229440.07
151C231340.06
152E231340.06
161C228140.08
162F228140.08
171C231120.07
172G231120.07
181C225740.09
182H225740.09
191D230540.07
192E230540.07
201D229640.08
202F229640.08
211D229940.08
212G229940.08
221D225840.1
222H225840.1
231E229720.08
232F229720.08
241E235700.07
242G235700.07
251E225700.08
252H225700.08
261F230060.09
262G230060.09
271F228040.09
272H228040.09
281G232100.09
282H232100.09
LS refinement shellResolution: 2.653→2.721 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 245 -
Rwork0.314 4084 -
obs--96.16 %
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)
10.4439-0.1895-0.15150.8024-0.14050.3623-0.01720.0050.032-0.0157-0.0265-0.00340.0075-0.00630.04370.20620.00180.00220.124-0.00520.10337.159147.9541.5836
20.1226-0.0755-0.10620.1674-0.02150.1596-0.00450.0138-0.01480.0140.0053-0.00420.0006-0.0192-0.00080.2018-0.0069-0.00270.1289-0.00270.111411.715820.546242.4649
31.1971.17770.19351.17760.16330.07060.0109-0.02110.03140.0381-0.03850.0201-0.03480.01960.02760.2369-0.0161-0.01110.1170.00980.115235.777544.276956.3116
40.07190.0818-0.02050.20070.0180.2564-0.0034-0.00710.00010.0015-0.0004-0.00930.01420.02770.00380.19760.0043-0.00040.13520.0010.113230.327819.514546.201
50.3176-0.0344-0.06751.0394-0.59590.3708-0.06760.10540.0569-0.00560.08350.0263-0.003-0.0648-0.01590.2809-0.0256-0.02060.1512-0.00220.089127.735797.251-6.9947
60.23160.0028-0.15370.0061-0.03060.32350.0134-0.01180.0093-0.0048-0.0161-0.0027-0.0353-0.00550.00270.23380.00680.00280.1421-0.00550.091623.403393.595319.6026
70.3758-0.00130.16610.57620.08830.0885-0.02070.0542-0.03830.01680.0606-0.0755-0.01040.027-0.03990.22230.00660.01410.1833-0.02650.097737.874265.88970.3362
80.3009-0.1502-0.30870.08020.15880.3251-0.0108-0.0113-0.00370.03560.01930.00140.02340.0437-0.00850.2380.00520.00650.156100.113424.876675.163422.3544
90.32150.1755-0.56141.02350.30351.41050.0556-0.02330.0295-0.05760.0748-0.0076-0.21410.1005-0.13030.263-0.01770.03310.1788-0.0150.1271-0.305440.773520.1631
104.58631.08380.01770.2592-0.00420.02850.0648-0.23530.67220.0535-0.04290.172-0.1345-0.0157-0.02190.65670.00350.05810.36670.14820.2227-24.581329.903913.9607
110.3109-0.3462-0.21020.69610.60230.5996-0.0173-0.0055-0.03040.05060.04130.00170.04750.1046-0.02390.22170.0093-0.02030.1641-0.01760.10674.07328.404119.7518
120.3718-0.11570.00230.1120.02560.28460.02030.0699-0.0165-0.0269-0.01680.00030.0250.0025-0.00350.2124-0.0002-0.00540.1465-0.01650.1031-20.635512.21618.9836
131.20411.3074-0.27831.4204-0.30320.0687-0.10870.1075-0.0422-0.10150.1073-0.04310.0251-0.00340.00140.2831-0.0253-0.01770.1175-0.01640.11719.546295.110656.78
140.09080.0367-0.04010.13090.13430.21730.02470.01390.0271-0.03280.0113-0.0233-0.0556-0.0005-0.0360.21670.00790.01210.12440.00090.126-5.282683.107856.0549
150.3253-0.19980.20832.33261.18270.9172-0.0227-0.00030.1550.18150.1463-0.50910.06250.0972-0.12360.22270.0003-0.04890.127-0.03080.24723.802265.115569.4046
160.3648-0.1641-0.07630.31170.07790.22830.0098-0.01040.0109-0.01320.0103-0.0163-0.00930.006-0.02010.2016-0.00410.00050.1223-0.0080.1201-1.016964.513158.3221
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 54
2X-RAY DIFFRACTION2A55 - 205
3X-RAY DIFFRACTION3B7 - 54
4X-RAY DIFFRACTION4B55 - 205
5X-RAY DIFFRACTION5C5 - 54
6X-RAY DIFFRACTION6C55 - 205
7X-RAY DIFFRACTION7D7 - 54
8X-RAY DIFFRACTION8D55 - 205
9X-RAY DIFFRACTION9E8 - 54
10X-RAY DIFFRACTION10E55 - 205
11X-RAY DIFFRACTION11F7 - 54
12X-RAY DIFFRACTION12F55 - 205
13X-RAY DIFFRACTION13G8 - 54
14X-RAY DIFFRACTION14G55 - 205
15X-RAY DIFFRACTION15H6 - 54
16X-RAY DIFFRACTION16H55 - 206

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