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- PDB-4b09: Structure of unphosphorylated BaeR dimer -

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Basic information

Entry
Database: PDB / ID: 4b09
TitleStructure of unphosphorylated BaeR dimer
ComponentsTRANSCRIPTIONAL REGULATORY PROTEIN BAER
KeywordsTRANSCRIPTION / RESPONSE REGULATOR / DNA BINDING
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / Transcriptional regulatory protein BaeR
Similarity search - Component
Biological speciesESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsChoudhury, H. / Beis, K.
CitationJournal: Protein Sci. / Year: 2013
Title: The Dimeric Form of the Unphosphorylated Response Regulator Baer.
Authors: Choudhury, H.G. / Beis, K.
History
DepositionJun 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
B: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
C: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
D: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
E: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
F: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
G: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
H: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
I: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
J: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
K: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
L: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,57321
Polymers335,17212
Non-polymers18,4019
Water00
1
A: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
B: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9514
Polymers55,8622
Non-polymers4,0892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-21.3 kcal/mol
Surface area24220 Å2
MethodPISA
2
C: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
D: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9514
Polymers55,8622
Non-polymers4,0892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-19.9 kcal/mol
Surface area24200 Å2
MethodPISA
3
E: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
F: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9514
Polymers55,8622
Non-polymers4,0892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-18.8 kcal/mol
Surface area24250 Å2
MethodPISA
4
G: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
H: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9073
Polymers55,8622
Non-polymers2,0451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-15.8 kcal/mol
Surface area24300 Å2
MethodPISA
5
I: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
J: TRANSCRIPTIONAL REGULATORY PROTEIN BAER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9073
Polymers55,8622
Non-polymers2,0451
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-20.2 kcal/mol
Surface area24250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.602, 130.401, 198.213
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
12
22
32
42
52
62

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 9:126)
211CHAIN C AND (RESSEQ 9:126)
311CHAIN E AND (RESSEQ 9:126)
411CHAIN G AND (RESSEQ 9:126)
511CHAIN I AND (RESSEQ 9:126)
611CHAIN K AND (RESSEQ 9:126)
112CHAIN B AND (RESSEQ 9:80 OR RESSEQ 100:125)
212CHAIN D AND (RESSEQ 9:80 OR RESSEQ 100:125)
312CHAIN F AND (RESSEQ 9:80 OR RESSEQ 100:125)
412CHAIN H AND (RESSEQ 9:80 OR RESSEQ 100:125)
512CHAIN J AND (RESSEQ 9:80 OR RESSEQ 100:125)
612CHAIN L AND (RESSEQ 9:80 OR RESSEQ 100:125)

NCS ensembles :
ID
1
2

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Components

#1: Protein
TRANSCRIPTIONAL REGULATORY PROTEIN BAER


Mass: 27931.006 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI STR. K-12 SUBSTR. MG1655 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P69229
#2: Chemical
ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Br12Ta6

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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: 4.56 Å3/Da / Density % sol: 75.88 % / Description: NONE
Crystal growpH: 8.4
Details: 1.2 M SODIUM ACETATE AND 0.1 M SODIUM CACODYLATE, PH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.3→76.23 Å / Num. obs: 89499 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.9 / % possible all: 98.6

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
PHENIX1.7.3_928refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.3→49.549 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 25.31 / Stereochemistry target values: ML
Details: LINKER REGION BETWEEN 126-141 IS MISSING THERE IS DENSITY BUT TOO POOR TO BUILD THE LINKER RELIABLY.
RfactorNum. reflection% reflection
Rfree0.2448 4488 5 %
Rwork0.2252 --
obs0.2262 89468 98.59 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.903 Å2 / ksol: 0.328 e/Å3
Refinement stepCycle: LAST / Resolution: 3.3→49.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21096 0 162 0 21258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321789
X-RAY DIFFRACTIONf_angle_d1.05530630
X-RAY DIFFRACTIONf_dihedral_angle_d14.48544
X-RAY DIFFRACTIONf_chiral_restr0.0443348
X-RAY DIFFRACTIONf_plane_restr0.0023708
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A935X-RAY DIFFRACTIONPOSITIONAL
12C935X-RAY DIFFRACTIONPOSITIONAL0.003
13E935X-RAY DIFFRACTIONPOSITIONAL0.004
14G935X-RAY DIFFRACTIONPOSITIONAL0.004
15I935X-RAY DIFFRACTIONPOSITIONAL0.004
16K935X-RAY DIFFRACTIONPOSITIONAL0.004
21B777X-RAY DIFFRACTIONPOSITIONAL
22D777X-RAY DIFFRACTIONPOSITIONAL0.003
23F777X-RAY DIFFRACTIONPOSITIONAL0.006
24H777X-RAY DIFFRACTIONPOSITIONAL0.006
25J777X-RAY DIFFRACTIONPOSITIONAL0.007
26L777X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.33750.33121380.35212811X-RAY DIFFRACTION99
3.3375-3.37680.33151430.33312829X-RAY DIFFRACTION98
3.3768-3.41790.36831590.35192775X-RAY DIFFRACTION98
3.4179-3.46120.36811580.32432829X-RAY DIFFRACTION99
3.4612-3.50670.31141590.3182770X-RAY DIFFRACTION99
3.5067-3.55470.33131270.29232857X-RAY DIFFRACTION98
3.5547-3.60550.2961500.28822790X-RAY DIFFRACTION98
3.6055-3.65930.26071510.27862832X-RAY DIFFRACTION99
3.6593-3.71650.28911480.26582817X-RAY DIFFRACTION99
3.7165-3.77740.32291570.25972801X-RAY DIFFRACTION99
3.7774-3.84250.26221400.24832857X-RAY DIFFRACTION99
3.8425-3.91230.23271340.23862793X-RAY DIFFRACTION98
3.9123-3.98760.26421460.24292882X-RAY DIFFRACTION99
3.9876-4.06890.25571350.23292805X-RAY DIFFRACTION99
4.0689-4.15730.2151370.21522844X-RAY DIFFRACTION99
4.1573-4.2540.22431570.20922823X-RAY DIFFRACTION99
4.254-4.36030.22081560.20952822X-RAY DIFFRACTION99
4.3603-4.47810.2451670.22822X-RAY DIFFRACTION99
4.4781-4.60980.20881440.192812X-RAY DIFFRACTION98
4.6098-4.75850.19781640.18932820X-RAY DIFFRACTION99
4.7585-4.92840.20611340.19152848X-RAY DIFFRACTION99
4.9284-5.12560.22581430.19922862X-RAY DIFFRACTION99
5.1256-5.35860.2281590.21972824X-RAY DIFFRACTION99
5.3586-5.64070.27021400.23582885X-RAY DIFFRACTION99
5.6407-5.99360.27011530.22682822X-RAY DIFFRACTION99
5.9936-6.45540.26431640.2362865X-RAY DIFFRACTION99
6.4554-7.10340.24361440.22562870X-RAY DIFFRACTION99
7.1034-8.12730.22141650.19962841X-RAY DIFFRACTION99
8.1273-10.22480.20491570.17722880X-RAY DIFFRACTION99
10.2248-49.55450.23961590.22292892X-RAY DIFFRACTION97
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)
19.59014.3614-0.78538.5032-1.1734.023-0.26560.58891.1991-0.3560.15240.0379-0.5883-0.14470.11240.54110.142-0.03680.550.06540.6005-20.7529-37.5364-102.5748
29.44260.1629-1.52748.54412.39825.7139-0.28260.6907-0.4263-0.01310.2212-0.1101-0.06090.2690.04350.99250.22670.01180.6534-0.02460.5017-22.0585-41.0102-50.9048
36.04035.6818-0.62359.609-0.64821.6685-0.43110.5768-0.4772-0.90090.3174-0.28810.3976-0.4530.13030.6390.0362-0.00720.7866-0.07080.6586-24.0897-63.5926-100.5786
47.2357-4.04390.60299.7558-0.57627.05810.37591.2313-1.1753-1.1338-0.36340.08121.70131.0926-0.08341.55630.52280.1081.1903-0.17830.9968-17.3268-70.5461-57.4864
59.9588-0.6881.925.07740.01563.04280.13590.4352-0.3527-0.2742-0.11830.72820.5146-0.1395-0.04850.7412-0.0085-0.01280.4857-0.01660.5293-46.3394-22.4294-36.6167
65.91180.3385-0.4096.7994-0.4232.9225-0.1083-0.2584-0.84280.6614-0.01120.86870.1303-0.50890.09220.56050.05590.09770.76480.04020.6759-69.471813.5607-29.4077
76.65692.84842.60073.79491.69545.50460.0726-0.2551-0.38251.1130.0319-0.74150.82750.7169-0.07921.1470.3951-0.13440.85040.04160.8519-11.5429-56.4585-29.5025
85.38560.62830.36216.65121.93285.1928-0.28751.1133-0.7124-0.49040.3999-1.04750.33761.27-0.12630.53780.0880.11981.2218-0.11090.8865-48.82614.936-102.7769
95.5258-0.8748-2.0093.50250.66544.13740.168-0.70091.2270.5294-0.0403-0.0438-1.50770.6795-0.20361.6845-0.4295-0.11880.8681-0.11431.1223-34.2113-4.534636.2357
107.5905-2.0696-1.64377.3928-1.73858.25540.19920.74780.4998-0.6407-0.3086-0.3419-0.69940.05680.01820.9501-0.2698-0.00890.69820.11360.6549-42.3916-21.761915.0909
118.555-0.35183.46198.8798-0.588.0193-0.1443-0.63470.14520.85940.06-0.25110.18530.08690.07070.4287-0.0165-0.0140.959-0.06030.5057-67.389417.1118-81.4849
128.30420.6873-1.20238.90632.65148.77850.3798-0.76350.64440.5925-0.0477-0.0832-0.1713-0.1414-0.33440.44540.09060.11720.9638-0.01520.6154-7.2715-49.7613-80.871
137.0179-0.53274.17078.2828-0.91349.40140.12860.6822-0.3402-0.81110.02170.16790.13690.3987-0.14970.71580.2511-0.00820.77290.07930.5603-52.08149.0794-51.1104
148.10810.30020.16115.5823-2.37057.8030.027-0.9798-0.19780.64310.25180.46360.0569-0.1238-0.25321.18510.25560.02840.62250.09270.6462-43.2267-4.6975-14.7682
158.54860.46980.59110.7307-0.40342.0552-0.00230.90470.173-0.1346-0.0735-0.22170.20810.62740.05960.97080.1552-0.01650.79970.04630.7995-22.5916-11.2971-34.4631
163.5253.3444-0.34379.28931.21012.6502-0.0617-0.45970.16980.5437-0.0448-0.0466-0.35860.18220.11890.60540.1148-0.0850.74340.01930.7106-49.637330.7259-31.4036
175.6534.29671.14583.26270.77482.6243-0.2231-0.2226-0.35250.52290.01960.04540.4494-0.15870.23911.07210.24390.17420.65610.07940.9574-36.3865-62.1624-36.7164
181.25732.7579-0.10296.42640.35532.42790.01410.13590.6452-0.2099-0.35460.2202-0.69340.4010.36130.8246-0.0629-0.12021.0770.0661.2594-55.45739.6788-96.487
192.0646-2.8371-0.90660.8439-0.15981.9092-0.3822-0.29380.46080.07830.0847-0.5393-0.38070.97030.29440.9104-0.3008-0.11791.2104-0.03631.254-16.809-23.427830.1835
207.01393.8098-2.19812.0935-1.52917.5005-0.34161.00560.6669-0.81270.334-0.9477-2.14991.5204-0.08282.0252-0.7878-0.10921.50420.28471.5069-18.6082-3.42118.5752
217.5109-1.1817-0.98156.383-1.21747.9268-0.0781-0.53820.55890.91730.2171-1.424-0.43912.1582-0.1220.7287-0.1175-0.26851.7032-0.05361.0599-39.475727.5099-74.9627
228.5635-1.6747-1.69716.6278-0.84547.7764-0.0275-1.36890.04671.00080.48470.8321-0.2811-1.409-0.40320.75090.27460.10011.6040.04880.6313-37.7896-49.6783-78.4894
238.9131-2.0032-0.03184.9202-0.12236.03220.46111.53620.7848-1.1307-0.1160.4261-1.2643-0.9469-0.37451.11810.3589-0.05841.23170.15970.6974-68.665534.5716-53.537
244.8752-1.01511.70467.5977-1.6829.94610.2185-0.86-0.61811.41890.1766-0.30751.29720.4362-0.36761.63980.2075-0.14610.74580.0860.6862-27.1942-30.6632-12.5339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND ((RESSEQ 9:126))
2X-RAY DIFFRACTION2CHAIN A AND ((RESSEQ 141:240))
3X-RAY DIFFRACTION3CHAIN B AND ((RESSEQ 9:125))
4X-RAY DIFFRACTION4CHAIN B AND ((RESSEQ 142:240))
5X-RAY DIFFRACTION5CHAIN C AND ((RESSEQ 9:126))
6X-RAY DIFFRACTION6CHAIN E AND ((RESSEQ 9:126))
7X-RAY DIFFRACTION7CHAIN G AND ((RESSEQ 9:126))
8X-RAY DIFFRACTION8CHAIN I AND ((RESSEQ 9:126))
9X-RAY DIFFRACTION9CHAIN K AND ((RESSEQ 9:126))
10X-RAY DIFFRACTION10CHAIN C AND ((RESSEQ 141:240))
11X-RAY DIFFRACTION11CHAIN E AND ((RESSEQ 141:240))
12X-RAY DIFFRACTION12CHAIN G AND ((RESSEQ 141:240))
13X-RAY DIFFRACTION13CHAIN I AND ((RESSEQ 141:240))
14X-RAY DIFFRACTION14CHAIN K AND ((RESSEQ 141:240))
15X-RAY DIFFRACTION15CHAIN D AND ((RESSEQ 9:125))
16X-RAY DIFFRACTION16CHAIN F AND ((RESSEQ 9:125))
17X-RAY DIFFRACTION17CHAIN H AND ((RESSEQ 9:125))
18X-RAY DIFFRACTION18CHAIN J AND ((RESSEQ 9:125))
19X-RAY DIFFRACTION19CHAIN L AND ((RESSEQ 9:125))
20X-RAY DIFFRACTION20CHAIN D AND ((RESSEQ 142:240))
21X-RAY DIFFRACTION21CHAIN F AND ((RESSEQ 142:240))
22X-RAY DIFFRACTION22CHAIN H AND ((RESSEQ 142:240))
23X-RAY DIFFRACTION23CHAIN J AND ((RESSEQ 142:240))
24X-RAY DIFFRACTION24CHAIN L AND ((RESSEQ 142:240))

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