[English] 日本語
Yorodumi
- PDB-7jve: Crystal structure of Salmonella enterica Typhimurium BcfH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jve
TitleCrystal structure of Salmonella enterica Typhimurium BcfH
ComponentsDsbA family protein
KeywordsOXIDOREDUCTASE / isomerase / fimbrial operon / virulence factor
Function / homologyDSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily / oxidoreductase activity / TRIETHYLENE GLYCOL / DsbA family protein
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.31 Å
AuthorsSubedi, P. / Heras, B. / Hor, L. / Paxman, J.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)180102987 Australia
Australian Research Council (ARC)130100580 Australia
CitationJournal: Antioxid.Redox Signal. / Year: 2021
Title: Salmonella enterica BcfH Is a Trimeric Thioredoxin-Like Bifunctional Enzyme with Both Thiol Oxidase and Disulfide Isomerase Activities.
Authors: Subedi, P. / Paxman, J.J. / Wang, G. / Hor, L. / Hong, Y. / Verderosa, A.D. / Whitten, A.E. / Panjikar, S. / Santos-Martin, C.F. / Martin, J.L. / Totsika, M. / Heras, B.
History
DepositionAug 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DsbA family protein
B: DsbA family protein
C: DsbA family protein
D: DsbA family protein
E: DsbA family protein
F: DsbA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,40030
Polymers165,9736
Non-polymers1,42724
Water16,718928
1
A: DsbA family protein
B: DsbA family protein
C: DsbA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,70615
Polymers82,9863
Non-polymers72012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12170 Å2
ΔGint-70 kcal/mol
Surface area30920 Å2
MethodPISA
2
D: DsbA family protein
E: DsbA family protein
F: DsbA family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,69415
Polymers82,9863
Non-polymers70712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-45 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.012, 133.731, 146.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
DsbA family protein / Thiol-disulfide isomerase / Thioredoxin domain-containing protein


Mass: 27662.166 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: B9C96_12120, CC725_14640, D7O80_18050, DOC60_06685, DSM38_01995, ECA50_10820, SAMEA4398682_04006
Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A564XRN6
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 0.2 M MgCl2, 0.1 mM Bis Tris propane, pH 6.0, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 88024 / % possible obs: 99.1 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.025 / Rrim(I) all: 0.077 / Χ2: 1.019 / Net I/σ(I): 13 / Num. measured all: 763336
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.346.30.58541770.8050.2450.6380.894.7
2.34-2.386.40.50142140.8330.2060.5440.8196.1
2.38-2.436.60.45743090.8640.1860.4960.82898.2
2.43-2.486.50.40442580.8880.1650.4380.82597.7
2.48-2.536.30.35142490.9110.1460.3820.80996.6
2.53-2.596.80.30343670.9370.1220.3280.82298.9
2.59-2.667.50.25743890.9560.0990.2760.83899.8
2.66-2.737.70.21643950.9710.0820.2320.84100
2.73-2.8180.19243990.9790.0720.2060.85799.8
2.81-2.98.30.16644030.9850.060.1770.90399.9
2.9-38.70.13544220.990.0480.1430.941100
3-3.129.20.11344230.9930.0390.1191.006100
3.12-3.269.80.09744260.9960.0320.1021.118100
3.26-3.4410.20.08144300.9960.0270.0861.214100
3.44-3.6510.60.06844750.9980.0220.0721.298100
3.65-3.9310.50.05844320.9980.0190.0611.324100
3.93-4.339.60.0544550.9980.0160.0531.31599.9
4.33-4.9510.60.04645240.9980.0150.0481.239100
4.95-6.2411.50.04445400.9980.0130.0461.012100
6.24-5011.30.03447370.9990.010.0360.87899.6

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
Cootmodel building
Auto-Rickshawphasing
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.31→42.65 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 4312 4.97 %
Rwork0.1665 82494 -
obs0.1686 86806 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 153.86 Å2 / Biso mean: 40.1789 Å2 / Biso min: 16.14 Å2
Refinement stepCycle: final / Resolution: 2.31→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11445 0 204 928 12577
Biso mean--48.87 38.43 -
Num. residues----1487
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.340.25651140.18251966208070
2.34-2.360.261210.1952411253287
2.36-2.390.25861240.19412448257288
2.39-2.420.22011350.19522590272592
2.42-2.460.26271460.19672651279795
2.46-2.490.26491430.19292643278696
2.49-2.520.26371210.19472703282496
2.52-2.560.20961350.19722705284097
2.56-2.60.28011390.19112777291699
2.6-2.650.26461450.186527862931100
2.65-2.690.24681700.185427582928100
2.69-2.740.21961600.185527732933100
2.74-2.790.23841300.19228352965100
2.79-2.850.24391570.191327992956100
2.85-2.910.25871450.196428022947100
2.91-2.980.19871300.185828332963100
2.98-3.050.25051740.176527992973100
3.05-3.140.22161560.178128042960100
3.14-3.230.21791530.177328032956100
3.23-3.330.2221350.172328592994100
3.33-3.450.21391440.173328172961100
3.45-3.590.23521460.163628262972100
3.59-3.750.21421540.163328342988100
3.75-3.950.19351410.144928422983100
3.95-4.20.19371590.138928302989100
4.2-4.520.17661370.130128633000100
4.52-4.980.14061360.131529063042100
4.98-5.70.17651600.149828633023100
5.7-7.170.20921320.17929403072100
7.17-42.650.14921700.152630283198100
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)
11.4321.7280.55353.00532.41293.6998-0.215-0.1926-0.2301-0.12270.2655-0.64470.0721.08410.36310.5166-0.0783-0.05420.65970.47050.732952.981633.84733.4063
21.25150.6213-0.69710.54-1.04921.67220.1264-0.05060.2208-0.0989-0.2426-0.2846-0.00430.40240.0960.2512-0.01980.0410.30290.10780.442933.408918.056717.3578
30.34590.41190.2091.0727-0.44743.21390.2211-0.13860.40070.27870.18990.1845-0.6314-0.1519-0.43230.30580.06590.07420.2181-0.0530.36552.232723.568938.4606
42.9863-0.5055-0.28383.19961.02052.7538-0.0733-0.222-0.08170.312-0.0457-0.0238-0.0180.17650.10660.1912-0.01790.01230.26190.02140.18367.280710.254738.8115
52.659-0.1557-0.38352.5220.56793.797-0.1145-0.1005-0.31330.0641-0.04210.04090.2646-0.12970.12510.1841-0.0060.01850.19720.02510.2371-4.5883.053437.3351
62.47791.6223-0.93772.2872-1.12181.88880.0636-0.13220.1073-0.0445-0.08760.20030.0567-0.13450.00760.21470.0308-0.01720.2313-0.03440.2364-8.92129.832729.3605
73.5197-0.26210.28512.5578-0.58723.5153-0.0149-0.19990.631-0.25210.0449-0.395-1.02290.11770.03940.3422-0.00010.07050.157-0.01740.339810.484821.624233.0671
84.2319-0.30950.7134.7334-0.21387.27980.0731-0.57570.43570.34430.1311-0.8261-0.57570.6141-0.20020.2481-0.0793-0.01310.3599-0.07870.332317.667818.973740.3314
90.58710.56530.37451.5799-1.03260.80190.04220.21960.21870.159-0.2433-0.1978-0.21550.20060.13950.32390.0050.10490.39350.15050.431545.79211.752213.194
102.87091.96920.22594.6141-0.04622.04410.0373-0.12660.1476-0.0426-0.14140.06650.0538-0.00730.10090.2218-0.01470.01450.14790.02430.203530.6869-29.063128.7986
113.5081.487-3.48916.5195-0.68536.7473-0.16290.2840.1071-0.82810.1027-1.13090.14240.58230.03390.344-0.03330.14230.31030.04570.508146.8456-22.40318.3249
122.04621.8682-0.3343.4393-0.24791.4417-0.1270.39360.1835-0.232-0.0475-0.13010.00470.3540.10580.30270.07870.08610.46990.22520.437942.075419.53867.9213
133.78960.49610.80252.6055-0.24095.0942-0.0580.4706-0.2557-0.4044-0.11830.32830.06250.14430.23720.27860.05380.02390.3213-0.03390.335121.4001-4.60379.3584
141.5516-0.2575-0.0571.9546-0.07112.26350.0128-0.0133-0.21450.0323-0.0617-0.01570.05670.09050.03430.17980.0230.04330.20070.0350.281622.967-1.862324.2587
157.11440.90970.65183.1116-0.17436.9731-0.12920.9812-0.369-1.0365-0.06970.2820.1503-0.46210.14660.46970.0412-0.02330.4387-0.07460.340516.3199-4.98323.2182
160.09260.219-0.13961.02060.46913.42750.1337-1.8665-0.49670.6645-0.42470.14090.01-0.3913-0.00720.7363-0.28930.0661.65740.03710.36750.46313.448243.9647
172.98212.37260.7561.82780.27590.97820.0943-0.66130.38260.0072-0.28330.3753-0.097-0.31080.11970.25750.03690.05860.3245-0.11840.362867.342716.229924.5183
183.2187-0.9534-0.07842.1043-0.20353.20520.10840.13490.8804-0.1856-0.1357-0.2053-0.69790.39780.00920.3519-0.04610.00280.1738-0.02460.362190.124231.096414.4661
193.0429-0.7867-0.41371.92770.03011.7689-0.02520.38530.1673-0.269-0.0473-0.0022-0.08680.02520.09640.2448-0.00850.0050.2560.04610.165690.230519.00866.9913
203.7168-0.3524-0.5492.1996-0.0052.3452-0.1890.8178-0.181-0.5455-0.0563-0.24450.36440.08610.15280.40790.06860.11360.46090.00360.239597.179813.9157-0.1211
212.83221.6251-2.65183.8016-3.34156.9002-0.00340.49280.0296-0.4655-0.0817-0.71380.70950.6190.30460.32960.10360.10710.44830.05810.3985110.547914.8265.7555
223.6136-0.838-0.01032.0756-0.76632.2182-0.1332-0.17690.3895-0.00710.07230.0792-0.2484-0.13610.01540.28570.0056-0.01990.1626-0.02990.217685.503922.285117.2951
234.2528-0.8133-1.64115.16590.68014.9714-0.45980.46990.6273-0.4102-0.05780.9489-0.5002-0.7269-0.13310.43340.1054-0.13110.34730.1110.461574.225429.54917.5745
240.2828-0.1551-0.71441.7119-0.71453.18210.4503-1.11520.36760.4306-0.02570.58810.2422-1.1148-0.21510.623-0.12130.18231.68-0.13550.532446.37186.167940.4107
257.1065-5.89234.23897.5478-2.86518.2981-0.1095-0.79380.29440.5381-0.2289-1.16410.31390.29020.16240.4664-0.22350.00640.79520.01260.334268.92451.115935.2656
264.32580.47241.03464.0373-0.4342.42130.5742-0.5552-1.41130.6005-0.2264-0.0420.9373-0.4475-0.36830.6353-0.1891-0.22940.40030.25210.903972.1389-18.287326.5832
275.2571-0.90661.21172.1642-0.85173.06420.296-0.0495-0.6409-0.06690.2614-0.1020.41710.074-0.29950.2224-0.0103-0.06220.2646-0.04470.394376.7994-6.431817.0952
284.9262-0.46231.4962.7459-0.15372.76990.27160.36-0.5098-0.1049-0.0376-0.17020.12090.2665-0.31440.2181-0.022-0.01120.1992-0.04920.235979.1054-4.663917.4356
293.3504-0.27551.33465.72962.40873.71590.02490.1124-0.3804-0.15390.2735-0.13870.0850.1406-0.28540.153-0.04170.02430.2151-0.01170.177672.7852.0349.873
302.73620.74991.01852.5994-0.78993.4187-0.12120.1114-0.105-0.17210.25260.1665-0.3008-0.2813-0.12240.18630.01440.0280.2571-0.0510.221165.37852.50988.4859
312.39171.0817-1.97256.98240.61566.02390.0136-0.2978-1.58890.38880.04920.12191.2761-0.153-0.0140.497-0.0779-0.20320.30520.03310.75176.2583-15.238423.2352
321.7653-0.346-1.89585.8186-0.33642.23030.3529-0.6961-1.14780.28570.2449-0.45841.03760.6595-0.41590.45110.0576-0.24640.45130.0620.585285.1338-13.292526.3646
331.90351.7329-1.05133.1233-1.30580.62820.4199-0.44570.79750.7671-0.67821.1086-0.7552-0.5005-0.02880.6937-0.12490.14831.63-0.33660.545150.3148.889942.227
340.90330.93-0.59061.66511.9595.3310.2027-0.1710.06160.0044-0.33590.0772-0.151-0.51280.20620.18510.05360.03480.34980.00170.277451.9522-7.95789.1032
353.51441.0766-1.23983.680.00274.7756-0.2149-0.5644-0.47960.41090.1427-0.02071.02230.40620.0380.52770.12020.06420.38850.03030.207657.5656-22.7761-3.8252
362.0044-0.9325-0.99741.72520.14364.0067-0.1636-0.5386-0.0130.26820.1545-0.2250.72290.6082-0.00710.32280.0927-0.0030.3283-0.01340.161162.8269-18.6493-11.1358
370.43680.40590.13061.29680.34754.0478-0.2028-0.69230.0621-0.09880.543-0.69450.25691.1499-0.1080.30240.1853-0.02760.5376-0.04260.290772.1425-17.733-17.6362
381.96950.249-1.27213.0674-1.31826.5482-0.1819-0.37590.0340.45820.17380.43560.2515-0.3195-0.00070.35310.07120.05810.3579-0.03050.225551.8467-14.656-0.4937
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 19 )A2 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 64 )A20 - 64
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 83 )A65 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 124 )A84 - 124
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 181 )A125 - 181
6X-RAY DIFFRACTION6chain 'A' and (resid 182 through 210 )A182 - 210
7X-RAY DIFFRACTION7chain 'A' and (resid 211 through 229 )A211 - 229
8X-RAY DIFFRACTION8chain 'A' and (resid 230 through 254 )A230 - 254
9X-RAY DIFFRACTION9chain 'B' and (resid 4 through 64 )B4 - 64
10X-RAY DIFFRACTION10chain 'B' and (resid 65 through 223 )B65 - 223
11X-RAY DIFFRACTION11chain 'B' and (resid 224 through 254 )B224 - 254
12X-RAY DIFFRACTION12chain 'C' and (resid 7 through 51 )C7 - 51
13X-RAY DIFFRACTION13chain 'C' and (resid 52 through 100 )C52 - 100
14X-RAY DIFFRACTION14chain 'C' and (resid 101 through 210 )C101 - 210
15X-RAY DIFFRACTION15chain 'C' and (resid 211 through 254 )C211 - 254
16X-RAY DIFFRACTION16chain 'D' and (resid 11 through 35 )D11 - 35
17X-RAY DIFFRACTION17chain 'D' and (resid 36 through 64 )D36 - 64
18X-RAY DIFFRACTION18chain 'D' and (resid 65 through 83 )D65 - 83
19X-RAY DIFFRACTION19chain 'D' and (resid 84 through 145 )D84 - 145
20X-RAY DIFFRACTION20chain 'D' and (resid 146 through 181 )D146 - 181
21X-RAY DIFFRACTION21chain 'D' and (resid 182 through 193 )D182 - 193
22X-RAY DIFFRACTION22chain 'D' and (resid 194 through 241 )D194 - 241
23X-RAY DIFFRACTION23chain 'D' and (resid 242 through 254 )D242 - 254
24X-RAY DIFFRACTION24chain 'E' and (resid 9 through 35 )E9 - 35
25X-RAY DIFFRACTION25chain 'E' and (resid 36 through 52 )E36 - 52
26X-RAY DIFFRACTION26chain 'E' and (resid 53 through 69 )E53 - 69
27X-RAY DIFFRACTION27chain 'E' and (resid 70 through 100 )E70 - 100
28X-RAY DIFFRACTION28chain 'E' and (resid 101 through 127 )E101 - 127
29X-RAY DIFFRACTION29chain 'E' and (resid 128 through 164 )E128 - 164
30X-RAY DIFFRACTION30chain 'E' and (resid 165 through 210 )E165 - 210
31X-RAY DIFFRACTION31chain 'E' and (resid 211 through 229 )E211 - 229
32X-RAY DIFFRACTION32chain 'E' and (resid 230 through 253 )E230 - 253
33X-RAY DIFFRACTION33chain 'F' and (resid 9 through 36 )F9 - 36
34X-RAY DIFFRACTION34chain 'F' and (resid 37 through 77 )F37 - 77
35X-RAY DIFFRACTION35chain 'F' and (resid 78 through 110 )F78 - 110
36X-RAY DIFFRACTION36chain 'F' and (resid 111 through 160 )F111 - 160
37X-RAY DIFFRACTION37chain 'F' and (resid 161 through 195 )F161 - 195
38X-RAY DIFFRACTION38chain 'F' and (resid 196 through 254 )F196 - 254

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more