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- PDB-5kew: Vibrio parahaemolyticus VtrA/VtrC complex bound to the bile salt ... -

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Basic information

Entry
Database: PDB / ID: 5kew
TitleVibrio parahaemolyticus VtrA/VtrC complex bound to the bile salt taurodeoxycholate
Components
  • VtrA Protein
  • VtrC Protein
KeywordsSIGNALING PROTEIN / heterodimer / alpha/beta / calycin beta barrel superfamily / bile salt receptor / taurodeoxycholate
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / membrane / metal ion binding
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 / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Taurodeoxycholate / ACETATE ION / Uncharacterized protein / Putative transcriptional regulator ToxR
Similarity search - Component
Biological speciesVibrio parahaemolyticus serotype O3:K6
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.103 Å
Model detailsThe C-terminal periplasmic domain of VtrA extends from residue 160 to 253. The C-terminal ...The C-terminal periplasmic domain of VtrA extends from residue 160 to 253. The C-terminal periplasmic domain of VtrC extends from residue 31 to 161.
AuthorsTomchick, D.R. / Orth, K. / Rivera-Cancel, G.
CitationJournal: Elife / Year: 2016
Title: Bile salt receptor complex activates a pathogenic type III secretion system.
Authors: Li, P. / Rivera-Cancel, G. / Kinch, L.N. / Salomon, D. / Tomchick, D.R. / Grishin, N.V. / Orth, K.
History
DepositionJun 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VtrA Protein
B: VtrC Protein
C: VtrA Protein
D: VtrC Protein
E: VtrA Protein
F: VtrC Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,36318
Polymers83,7046
Non-polymers2,65912
Water3,477193
1
A: VtrA Protein
B: VtrC Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1778
Polymers27,9012
Non-polymers1,2766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-25 kcal/mol
Surface area12430 Å2
MethodPISA
2
C: VtrA Protein
D: VtrC Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6896
Polymers27,9012
Non-polymers7884
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-37 kcal/mol
Surface area11680 Å2
MethodPISA
3
E: VtrA Protein
F: VtrC Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4974
Polymers27,9012
Non-polymers5962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-26 kcal/mol
Surface area12010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.385, 71.276, 203.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein VtrA Protein


Mass: 10982.484 Da / Num. of mol.: 3
Fragment: VtrA C-terminal periplasmic domain, UNP residues 161-253
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Strain: RIMD 2210633 / Gene: VPA1332 / Plasmid: pACYCDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87GI4
#2: Protein VtrC Protein


Mass: 16918.775 Da / Num. of mol.: 3
Fragment: VtrC C-terminal periplasmic domain, UNP residues 31-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) (bacteria)
Strain: RIMD 2210633 / Gene: VPA1333 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87GI3

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Non-polymers , 5 types, 205 molecules

#3: Chemical
ChemComp-6SB / Taurodeoxycholate / 2-[[(4~{R})-4-[(3~{R},5~{R},8~{R},9~{S},10~{S},12~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,12-bis(oxidanyl)-2,3,4,5,6 ,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoyl]amino]ethanesulfonic acid


Mass: 499.704 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H45NO6S
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.79 % / Mosaicity: 0.385 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate, 0.5 mM taurodeoxycholine, 22.5% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Feb 19, 2016 / Details: monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.1→35.638 Å / Num. obs: 45762 / % possible obs: 95.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 24.18 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.043 / Rrim(I) all: 0.09 / Χ2: 0.9 / Net I/av σ(I): 15.889 / Net I/σ(I): 9.4 / Num. measured all: 176526
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.142.80.362179.4
2.14-2.182.60.353182.3
2.18-2.222.90.312187.2
2.22-2.263.10.304190.8
2.26-2.313.20.306193.4
2.31-2.373.40.313194.6
2.37-2.423.50.339198.3
2.42-2.493.80.345199.1
2.49-2.563.90.312198.8
2.56-2.653.80.289197.8
2.65-2.744.40.239199.5
2.74-2.854.50.186199.9
2.85-2.984.40.147199.8
2.98-3.144.40.111199.9
3.14-3.334.30.083199.2
3.33-3.594.20.065197.2
3.59-3.954.50.059199.5
3.95-4.524.40.052199.7
4.52-5.74.10.047197.6
5.7-504.10.037197.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHENIX1.10.1_2155phasing
RefinementResolution: 2.103→35.638 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.33
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2000 4.84 %random
Rwork0.1965 ---
obs0.1982 41304 86.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.85 Å2 / Biso mean: 39.3728 Å2 / Biso min: 5.81 Å2
Refine analyzeLuzzati sigma a obs: 0.23 Å
Refinement stepCycle: final / Resolution: 2.103→35.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5411 0 361 193 5965
Biso mean--44.28 35.32 -
Num. residues----651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025711
X-RAY DIFFRACTIONf_angle_d0.4877757
X-RAY DIFFRACTIONf_chiral_restr0.048860
X-RAY DIFFRACTIONf_plane_restr0.002953
X-RAY DIFFRACTIONf_dihedral_angle_d11.3893327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.103-2.15550.2588910.21421807189857
2.1555-2.21370.25291030.21862011211462
2.2137-2.27890.27411120.20182189230169
2.2789-2.35240.29691210.20142378249974
2.3524-2.43650.26591290.20162538266779
2.4365-2.5340.22051400.21162750289085
2.534-2.64930.26211450.21652858300388
2.6493-2.78890.23211600.21423133329398
2.7889-2.96360.26971630.21732253388100
2.9636-3.19230.23941660.204832403406100
3.1923-3.51330.2131620.1973194335698
3.5133-4.0210.22281670.17932723439100
4.021-5.06380.18241680.15523296346499
5.0638-35.64310.23951730.21783413358698
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)
10.0416-0.0179-0.0520.01180.03480.13910.0839-0.0225-0.00780.00080.0538-0.09320.03250.09670.14340.066-0.0043-0.02170.1686-0.04310.1659-13.41510.46921.7426
20.09840.0512-0.00280.0348-0.02060.07490.0573-0.02460.0152-0.00180.0787-0.01210.0459-0.00250.2363-0.1219-0.1109-0.13240.0833-0.11040.1306-22.032513.369-2.2993
30.0066-0.0007-0.0130.0358-0.02320.12060.0089-0.014-0.0049-0.04070.0113-0.00960.1044-0.0217-0.03570.0226-0.0416-0.09810.0014-0.14110.0425-27.90226.647-15.4563
40.03880.0193-0.00820.0184-0.01130.00830.0267-0.0282-0.0177-0.02830.0115-0.01140.0033-0.05240.02180.12530.0892-0.02110.2447-0.06130.193-32.657611.0596-19.9325
50.01150.0191-0.01110.0348-0.01970.016-0.07870.0137-0.0567-0.05550.0666-0.04180.0488-0.01490.00690.14520.0697-0.01560.2469-0.06650.1817-22.37384.3238-23.7142
60.00660.00970.00110.0187-0.00630.0213-0.0041-0.00310.0156-0.11630.06350.01-0.0136-0.0185-0.00020.21060.0723-0.04910.2118-0.0390.1795-30.70839.4248-27.4332
70.0021-0.0077-0.00880.0260.03080.03770.05930.0989-0.0008-0.05540.0634-0.0665-0.05580.02590.00860.15920.0516-0.02690.2367-0.04440.2651-17.32587.8717-22.5298
80.10420.0145-0.04710.0076-0.00730.06140.06170.0545-0.0516-0.01220.0824-0.03930.0120.08650.05750.128-0.0039-0.05130.1425-0.04410.1905-19.33764.4539-13.3258
90.0051-0.0069-0.00640.02850.02940.03010.0114-0.00980.02260.00260.0129-0.01420.0563-0.0280.00540.1215-0.0414-0.06660.0671-0.070.1705-23.11570.1818-11.8174
100.0008-0.0005-0.00080.00070.00020.00070.00190.0016-0.00350.0092-0.0065-0.0143-0.00090.0102-00.23670.1005-0.06060.2592-0.05820.21967.4869-12.0643-47.8132
110.0007-0.000200.00010.00010.00540.07250.03030.00420.01650.0545-0.0018-0.016-0.0121-00.25620.0502-0.04380.1839-0.01850.1822-4.2963-4.0735-49.703
120.0016-0.0008-0.00090.0017-0.00150.00210.019-0.0102-0.0196-0.02140.02980.0288-0.0003-0.0553-00.23980.0496-0.04330.2124-0.06590.189-12.1895-5.2945-46.6441
130.00940.0011-0.00380.0004-0.00070.0031-0.0030.00380.0126-0.0039-0.01450.0075-0.00360.00100.26350.06260.01260.3165-0.04740.376-10.58018.0892-41.2237
140.0071-0.0018-0.00220.00130.00240.0037-0.0034-0.0012-0.0117-0.0006-0.0082-0.00240.0217-0.021400.1610.0365-0.02190.1697-0.02460.1381-0.7067-5.1911-40.7698
1500-00.0007-0.00010.00170.0002-0.00120.0025-0.0021-0.0006-0.008-0.0044-0.0018-00.59470.00520.00560.5362-0.07580.6466-0.617912.0149-39.6697
160.03810.0175-0.01070.017-0.00750.00610.0094-0.01570.0306-0.00360.00670.0051-0.02630.02370.00140.1798-0.0347-0.01190.214-0.04020.1284-0.2795-2.902-33.4784
170.0003-0.00030.00090.0002-0.00050.0010.0003-0.0105-0.0130.0040.001-0.0035-0.00250.008900.4503-0.0834-0.0720.4030.06320.4839-7.9105-17.1441-35.5006
180.00270.0003-0.00340.0024-0.00280.00540.0744-0.03130.02150.00410.03660.04680.0042-0.01960.00010.1618-0.02050.05350.2623-0.05640.2417-10.7688-3.8786-35.1889
190.0065-0.004-0.00010.01440.01780.0201-0.0159-0.0219-00.04350.0416-0.02640.0539-0.023700.2265-0.06250.00170.1928-0.01530.14117.1307-1.8724-31.4826
200.02220.00480.00210.0127-0.01380.02160.02560.00590.0270.09440.04920.03240.01320.04880.0010.2038-0.02920.01340.2649-0.04010.121212.4802-1.569-28.5368
210.02770.00150.00560.04170.00080.00240.060.0112-0.05770.11280.0205-0.1415-0.0321-0.0076-0.00370.22650.0014-0.03130.3222-0.05940.151418.8484-5.4555-33.9683
220.006-0.00650.00470.0046-0.00370.00290.0189-0.0183-0.0209-0.00480.00430.0242-0.0115-0.0047-00.41210.011-0.10120.298-0.00020.235318.5215-8.4288-23.2681
230.03320.0245-0.0110.0243-0.0130.00820.0210.02590.012-0.0080.01880.012-0.0066-0.00990.00490.23480.0138-0.00740.2021-0.07030.132411.2772-3.0825-46.5913
240.0106-0.00420.00290.00630.00720.01180.02660.03380.0052-0.0180.0113-0.02830.00090.0377-00.2094-0.0285-0.02780.1592-0.0070.12078.99150.4628-40.2923
250.00690.00570.00230.00430.00190.00150.00580.01370.02060.06220.02530.0146-0.0398-0.021800.33090.03030.0570.17040.01350.2498.66336.7595-15.9563
260.00420.003200.00410.00650.0180.0433-0.0138-0.00640.051-0.0042-0.0042-0.0108-0.01980.00010.5150.0312-0.00380.14060.01980.24489.829745.7833-11.5096
270.01460.0077-0.02870.0242-0.00160.0808-0.01570.05010.0829-0.0060.02460.0791-0.0664-0.0674-0.00490.23410.01290.00660.10460.02380.20778.075643.7309-24.7552
280.02480.0031-0.02370.0409-0.01020.02360.01630.0110.0175-0.00530.01440.0104-0.04530.0110.01290.4358-0.0684-0.09940.1765-0.02550.280516.471650.1194-19.8262
290.0052-0.0022-0.00320.0049-0.00330.0061-0.01870.00140.01840.0252-0.005-0.0058-0.0545-0.028200.1811-0.0539-0.01420.20110.04740.26529.082836.7487-37.4345
300.0178-0.0149-0.00450.01120.00030.01230.127-0.07240.0471-0.02530.0878-0.0682-0.0155-0.00450.00040.2958-0.08990.01240.24170.01280.236316.268137.7615-39.0277
310.0881-0.05220.05120.0371-0.02380.03020.06820.0271-0.0859-0.06770.09020.0465-0.01510.0850.01310.2592-0.00490.030.2026-0.01450.212316.682528.8697-39.3962
320.0045-0.0005-0.00560.00360.00070.006-0.0366-0.0032-0.0407-0.0072-0.0259-0.0058-0.0030.036900.3262-0.01220.07850.3240.00670.341525.621734.7787-45.7027
330.00210.0004-0.00180.0037-0.00330.00310.029-0.0140.00080.01550.04090.00160.0186-0.033800.23380.03370.0180.13530.02970.246310.852627.0516-28.3198
340.00470.0055-0.00990.0106-0.01260.01650.0384-0.0055-0.01150.02720.03680.0392-0.00180.0335-00.16730.0203-0.00560.22770.01450.13717.958134.2292-31.5782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 165 through 205 )A165 - 205
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 253 )A206 - 253
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 59 )B0 - 59
4X-RAY DIFFRACTION4chain 'B' and (resid 60 through 78 )B60 - 78
5X-RAY DIFFRACTION5chain 'B' and (resid 79 through 95 )B79 - 95
6X-RAY DIFFRACTION6chain 'B' and (resid 96 through 121 )B96 - 121
7X-RAY DIFFRACTION7chain 'B' and (resid 122 through 139 )B122 - 139
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 153 )B140 - 153
9X-RAY DIFFRACTION9chain 'B' and (resid 154 through 161 )B154 - 161
10X-RAY DIFFRACTION10chain 'C' and (resid 164 through 168 )C164 - 168
11X-RAY DIFFRACTION11chain 'C' and (resid 169 through 182 )C169 - 182
12X-RAY DIFFRACTION12chain 'C' and (resid 183 through 199 )C183 - 199
13X-RAY DIFFRACTION13chain 'C' and (resid 200 through 205 )C200 - 205
14X-RAY DIFFRACTION14chain 'C' and (resid 206 through 221 )C206 - 221
15X-RAY DIFFRACTION15chain 'C' and (resid 222 through 226 )C222 - 226
16X-RAY DIFFRACTION16chain 'C' and (resid 227 through 233 )C227 - 233
17X-RAY DIFFRACTION17chain 'C' and (resid 234 through 239 )C234 - 239
18X-RAY DIFFRACTION18chain 'C' and (resid 240 through 253 )C240 - 253
19X-RAY DIFFRACTION19chain 'D' and (resid 31 through 48 )D31 - 48
20X-RAY DIFFRACTION20chain 'D' and (resid 49 through 76 )D49 - 76
21X-RAY DIFFRACTION21chain 'D' and (resid 77 through 109 )D77 - 109
22X-RAY DIFFRACTION22chain 'D' and (resid 110 through 131 )D110 - 131
23X-RAY DIFFRACTION23chain 'D' and (resid 132 through 139 )D132 - 139
24X-RAY DIFFRACTION24chain 'D' and (resid 140 through 161 )D140 - 161
25X-RAY DIFFRACTION25chain 'E' and (resid 166 through 182 )E166 - 182
26X-RAY DIFFRACTION26chain 'E' and (resid 183 through 199 )E183 - 199
27X-RAY DIFFRACTION27chain 'E' and (resid 200 through 233 )E200 - 233
28X-RAY DIFFRACTION28chain 'E' and (resid 234 through 253 )E234 - 253
29X-RAY DIFFRACTION29chain 'F' and (resid 31 through 42 )F31 - 42
30X-RAY DIFFRACTION30chain 'F' and (resid 43 through 72 )F43 - 72
31X-RAY DIFFRACTION31chain 'F' and (resid 73 through 109 )F73 - 109
32X-RAY DIFFRACTION32chain 'F' and (resid 110 through 129 )F110 - 129
33X-RAY DIFFRACTION33chain 'F' and (resid 130 through 139 )F130 - 139
34X-RAY DIFFRACTION34chain 'F' and (resid 140 through 161 )F140 - 161

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