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- PDB-5h9t: Crystal structure of native NalD at resolution of 2.9, the second... -

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Basic information

Entry
Database: PDB / ID: 5h9t
TitleCrystal structure of native NalD at resolution of 2.9, the secondary repressor of MexAB-OprM multidrug efflux pump in Pseudomonas aeruginosa
ComponentsNalD
KeywordsTRANSCRIPTION REGULATOR / Repressor / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 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 Natural Science Foundation of China20721002 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. / Wang, D. / Zhou, W. / Sang, H. / Liu, X. / Ge, Z. / Zhang, J. / Lan, L. / Yang, C.G. / Chen, H.
History
DepositionDec 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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: NalD
B: NalD
C: NalD
D: NalD
E: NalD
F: NalD
G: NalD
H: NalD


Theoretical massNumber of molelcules
Total (without water)196,4338
Polymers196,4338
Non-polymers00
Water18010
1
A: NalD
B: NalD


Theoretical massNumber of molelcules
Total (without water)49,1082
Polymers49,1082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-18 kcal/mol
Surface area17330 Å2
MethodPISA
2
C: NalD
D: NalD


Theoretical massNumber of molelcules
Total (without water)49,1082
Polymers49,1082
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-18 kcal/mol
Surface area18090 Å2
MethodPISA
3
E: NalD
F: NalD


Theoretical massNumber of molelcules
Total (without water)49,1082
Polymers49,1082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-16 kcal/mol
Surface area17590 Å2
MethodPISA
4
G: NalD
H: NalD


Theoretical massNumber of molelcules
Total (without water)49,1082
Polymers49,1082
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-16 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.676, 127.602, 265.420
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
17GLUGLUTRPTRPAA6 - 2056 - 205
27GLUGLUTRPTRPHH6 - 2056 - 205
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
113ASPASPTRPTRPBB7 - 2057 - 205
213ASPASPTRPTRPHH7 - 2057 - 205
114ASPASPASPASPCC7 - 2047 - 204
214ASPASPASPASPDD7 - 2047 - 204
115SERSERASPASPCC8 - 2048 - 204
215SERSERASPASPEE8 - 2048 - 204
116ASPASPTRPTRPCC7 - 2057 - 205
216ASPASPTRPTRPFF7 - 2057 - 205
117SERSERTRPTRPCC8 - 2058 - 205
217SERSERTRPTRPGG8 - 2058 - 205
118GLUGLUTRPTRPCC6 - 2056 - 205
218GLUGLUTRPTRPHH6 - 2056 - 205
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
125SERSERTRPTRPEE8 - 2058 - 205
225SERSERTRPTRPHH8 - 2058 - 205
126SERSERTRPTRPFF8 - 2058 - 205
226SERSERTRPTRPGG8 - 2058 - 205
127ASPASPASPASPFF7 - 2047 - 204
227ASPASPASPASPHH7 - 2047 - 204
128SERSERASPASPGG8 - 2048 - 204
228SERSERASPASPHH8 - 2048 - 204

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: 24554.121 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: nalD, PA3574 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: tacsimate,sodium citrate tribasic dihydrate, polyethylene glycol 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: 2.89→50 Å / Num. obs: 47656 / % possible obs: 99.6 % / Redundancy: 9.3 % / Rsym value: 0.09 / Net I/σ(I): 32.46
Reflection shellResolution: 2.89→3 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.5 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DAJ
Resolution: 2.89→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 36.505 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25214 2411 5.1 %RANDOM
Rwork0.19397 ---
obs0.19699 45176 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.563 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å2-0 Å20 Å2
2--5.37 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.89→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12623 0 0 10 12633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01912862
X-RAY DIFFRACTIONr_bond_other_d0.0080.0212388
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.96517390
X-RAY DIFFRACTIONr_angle_other_deg1.745328283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.54951552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30723.014657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.434152275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.71415146
X-RAY DIFFRACTIONr_chiral_restr0.0810.21954
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114486
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023112
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.946325250
X-RAY DIFFRACTIONr_sphericity_free86.36151
X-RAY DIFFRACTIONr_sphericity_bonded20.775525020
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A117740.1
12B117740.1
21A109250.14
22C109250.14
31A111380.14
32D111380.14
41A111960.13
42E111960.13
51A110790.13
52F110790.13
61A111000.13
62G111000.13
71A111530.13
72H111530.13
81B109050.13
82C109050.13
91B110380.14
92D110380.14
101B113290.12
102E113290.12
111B110150.14
112F110150.14
121B112850.12
122G112850.12
131B112590.12
132H112590.12
141C105150.15
142D105150.15
151C105970.15
152E105970.15
161C103200.17
162F103200.17
171C103310.16
172G103310.16
181C105130.16
182H105130.16
191D109200.14
192E109200.14
201D105440.16
202F105440.16
211D104700.16
212G104700.16
221D105100.16
222H105100.16
231E107890.15
232F107890.15
241E110370.13
242G110370.13
251E109670.13
252H109670.13
261F105490.16
262G105490.16
271F107260.15
272H107260.15
281G109100.14
282H109100.14
LS refinement shellResolution: 2.887→2.961 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 138 -
Rwork0.249 2946 -
obs--88.27 %
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)
12.2899-1.86940.2862.0255-1.15651.88620.03410.00880.1717-0.0905-0.0999-0.14090.0918-0.02350.06580.44440.02430.01120.2343-0.06550.3937.087647.68341.4232
20.4492-0.4319-0.22370.5723-0.15661.05220.03350.1562-0.0538-0.0093-0.06010.02730.0684-0.30530.02660.3855-0.051-0.00830.23980.01140.405511.695420.268242.2978
34.38813.48940.68013.39551.56272.1820.0896-0.2620.2570.134-0.23250.1243-0.24640.13780.14290.4936-0.2319-0.07350.16840.03520.395435.619544.171256.1048
40.16930.1822-0.21240.6370.10161.3698-0.0397-0.1023-0.0501-0.0038-0.07650.04210.08840.26710.11620.36840.0168-0.00880.25640.0350.395730.332619.394946.002
53.0162-0.85110.3625.7052-5.13584.6814-0.25470.19910.22470.0910.2659-0.0285-0.0604-0.2557-0.01120.5029-0.1692-0.05310.36540.08450.151827.637896.9841-7.0272
61.15570.3768-0.71940.934-0.04432.4402-0.01020.05930.29710.20030.14950.263-0.17270.2199-0.13930.5170.06440.04330.2678-0.00350.21623.348493.019819.5803
71.8254-0.77290.86063.63141.9622.3192-0.22640.0102-0.03240.23550.4474-0.01270.06290.4487-0.22090.2943-0.010.04840.4445-0.16130.303337.728465.51660.3829
82.0104-0.1642-1.08111.05421.30492.0917-0.2666-0.0048-0.18680.33260.23220.04490.33750.27860.03440.56440.18130.11220.31920.00890.216324.74774.812122.3446
92.72672.213-0.97365.56142.93374.03830.0693-0.0615-0.0749-0.23830.2114-0.3227-0.36840.2909-0.28070.4918-0.0750.09180.2758-0.01720.2716-0.475940.820620.0157
102.4030.604-0.29430.5464-0.04110.70050.13420.2830.1013-0.05050.12490.1191-0.3427-0.0869-0.25910.44740.02190.07470.3470.12380.2501-24.723429.687413.8115
112.2861-3.0224-0.26994.1-0.18413.263-0.0723-0.25860.31990.10170.2307-0.37710.27990.4737-0.15840.2959-0.0046-0.08120.448-0.16840.31024.04338.331119.4075
121.015-0.4795-0.25621.0721-0.09650.44280.05190.2194-0.1976-0.1051-0.01640.08080.00110.0475-0.03550.3813-0.0124-0.04150.4041-0.08780.259-20.79311.84198.7135
136.06913.9174-1.58252.5363-1.0090.4699-0.45080.3424-0.3386-0.36450.2991-0.2686-0.09050.01670.15160.878-0.4295-0.06870.2484-0.11980.619419.54494.929356.5416
140.87090.3101-0.18020.73320.59940.96740.1340.01850.1026-0.30340.0352-0.082-0.3923-0.1083-0.16920.54980.06280.13330.1065-0.02550.4378-5.270582.891655.9374
153.0932-1.94431.65648.9094-2.87685.8469-0.2176-0.25120.26650.2924-0.0045-1.62030.07630.0320.2220.10260.0088-0.09810.1148-0.19570.813623.725364.861669.0041
160.8088-0.9081-0.10091.33260.54520.72730.0493-0.08570.0696-0.06790.1406-0.1209-0.0113-0.0155-0.18990.38250.00390.01910.1788-0.09860.4537-1.150464.109258.1427
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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