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- PDB-4h9v: Structure of Geobacillus kaustophilus lactonase, mutant E101G/R23... -

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Basic information

Entry
Database: PDB / ID: 4h9v
TitleStructure of Geobacillus kaustophilus lactonase, mutant E101G/R230C with Zn2+
ComponentsPhosphotriesterase
KeywordsHYDROLASE / (beta/alpha)8 barrel
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds / catabolic process / hydrolase activity / zinc ion binding
Similarity search - Function
Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / HYDROXIDE ION / Phosphotriesterase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.971 Å
AuthorsXue, B. / Chow, J.Y. / Yew, W.S. / Robinson, R.C.
CitationJournal: Biochemistry / Year: 2013
Title: Structural evidence of a productive active site architecture for an evolved quorum-quenching GKL lactonase.
Authors: Xue, B. / Chow, J.Y. / Baldansuren, A. / Yap, L.L. / Gan, Y.H. / Dikanov, S.A. / Robinson, R.C. / Yew, W.S.
History
DepositionSep 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotriesterase
B: Phosphotriesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7848
Polymers73,5082
Non-polymers2776
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-132 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.280, 130.208, 51.290
Angle α, β, γ (deg.)90.000, 96.330, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 3:99 or resseq 108:144 or resseq...A0
211chain 'B' and (resseq 3:99 or resseq 108:144 or resseq...B0

NCS oper: (Code: given
Matrix: (0.109742, -0.001545, -0.993959), (0.000823, -0.999998, 0.001645), (-0.99396, -0.000998, -0.109741)
Vector: 3.8037, 68.7117, 4.23395)

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Components

#1: Protein Phosphotriesterase


Mass: 36753.812 Da / Num. of mol.: 2 / Mutation: E101G,R230C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: GK1506 / Plasmid: pET-15b, modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5KZU5, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: sitting-drop vapor diffusion / pH: 7.5
Details: 100 mM Tris, pH 7.5, 20% (w/v) PEG 4000, 10% (v/v) glycerol, 0.1 mM ZnCl2, sitting-drop vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 43260 / Num. obs: 43260 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Χ2: 0.941 / Net I/σ(I): 18.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.97-22.90.2212920.911156.2
2-2.0430.19615510.881164.9
2.04-2.083.10.19616560.933171.1
2.08-2.123.20.17818770.914178.5
2.12-2.173.30.15419670.895185.6
2.17-2.223.30.14721650.947190.6
2.22-2.273.40.13222110.966195.2
2.27-2.343.50.12123560.944197.8
2.34-2.43.60.11522700.936199.4
2.4-2.483.80.10223530.9581100
2.48-2.573.80.09123660.9611100
2.57-2.673.80.07723600.9461100
2.67-2.83.80.06623510.921100
2.8-2.943.80.06123410.8911100
2.94-3.133.80.05523770.872199.9
3.13-3.373.80.05123370.827199.9
3.37-3.713.80.05923620.967199.7
3.71-4.243.70.06223851.122199.5
4.24-5.353.50.05423150.935199
5.35-503.70.0623681.036197.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.41 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å28.68 Å
Translation3.5 Å28.68 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.971→19.967 Å / Occupancy max: 1 / Occupancy min: 0.54 / SU ML: 0.21 / σ(F): 0 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 1961 5.09 %random
Rwork0.1825 ---
all0.1845 38503 --
obs0.1845 38503 81.87 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.618 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso max: 154.57 Å2 / Biso mean: 29.2734 Å2 / Biso min: 4.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.5154 Å20 Å20.7418 Å2
2--14.0552 Å2-0 Å2
3---5.8946 Å2
Refinement stepCycle: LAST / Resolution: 1.971→19.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 6 233 5253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085130
X-RAY DIFFRACTIONf_angle_d1.1026940
X-RAY DIFFRACTIONf_chiral_restr0.079752
X-RAY DIFFRACTIONf_plane_restr0.005910
X-RAY DIFFRACTIONf_dihedral_angle_d14.6061898
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2328X-RAY DIFFRACTIONPOSITIONAL0.026
12B2328X-RAY DIFFRACTIONPOSITIONAL0.026
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 (%)
1.9708-2.020.2382630.17751021108433
2.02-2.07460.2267630.19321324138741
2.0746-2.13550.251840.1991746183054
2.1355-2.20440.24351010.20322027212864
2.2044-2.28310.26041150.20142373248875
2.2831-2.37430.31421560.19862736289285
2.3743-2.48220.25381670.19773017318496
2.4822-2.61280.24431760.191231883364100
2.6128-2.77610.21941810.180631443325100
2.7761-2.98980.21921640.1932333397100
2.9898-3.28950.23331750.184131733348100
3.2895-3.76270.20271770.172731783355100
3.7627-4.73020.18351790.15143185336499
4.7302-19.96830.22251600.19763197335799
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)
10.0211-0.10830.01790.5757-0.07350.0456-0.0035-0.0814-0.05740.12840.0035-0.13410.06010.1127-0.11460.05140.0326-0.04750.30230.110.0901-1.168425.214941.6883
20.05820.01620.00950.0411-0.01710.0284-0.0107-0.007-0.0062-0.0537-0.02740.0265-0.0224-0.0089-0.03460.09630.0929-0.01150.08660.11020.165-10.948623.937918.7401
30.03570.08-0.09830.195-0.21860.2717-0.06780.03830.0261-0.0362-0.02370.08770.0406-0.0573-0.00040.1011-0.03590.01230.36850.07210.3518-21.716821.153823.7457
40.0624-0.03270.08560.018-0.0430.1963-0.0097-0.0405-0.0849-0.0225-0.0277-0.03280.07340.0395-0.04060.0626-0.02250.00310.11910.14960.2352-12.151112.122431.7148
50.23770.1722-0.07090.23360.10780.25290.0269-0.1356-0.17180.0199-0.0304-0.03270.17180.05580.00970.07620.0255-0.00180.06350.10730.1264-7.276225.130528.1106
60.20010.05770.06790.3393-0.02740.1008-0.00130.0005-0.0840.02-0.00370.0741-0.0011-0.05010.03360.05980.03060.03770.22370.07530.1766-15.700122.866236.249
70.32830.05490.15531.5207-0.46480.23150.00180.1032-0.0044-0.18370.004-0.10260.06270.01070.25110.04990.02310.02450.10790.06410.1093-4.541830.682623.6594
80.0059-0.002-0.00240.007-0.00350.0038-0.02230.0363-0.0539-0.04620.0008-0.00290.00240.0241-0.00030.35180.00090.01960.33550.01620.2765-1.578646.773211.9835
90.2967-0.12130.00280.2153-0.04610.0467-0.002-0.00110.2013-0.1113-0.0036-0.0847-0.22620.0626-0.03290.1207-0.0291-0.00550.0843-0.01740.1507-0.052943.500825.2127
100.11510.1658-0.17270.2422-0.25280.26220.04180.04770.04210.05790.04390.0486-0.1085-0.03580.0540.05180.05020.00960.1422-0.00360.035-3.737133.795528.4025
110.0095-0.00610.02090.1286-0.06790.08280.01760.13290.0786-0.0447-0.0413-0.02240.01060.0574-0.00990.12350.0527-0.01560.42490.01910.15979.225532.72839.7061
120.3462-0.0253-0.16010.129-0.12070.21050.0403-0.10110.120.0392-0.0657-0.029-0.04740.0936-0.04930.0172-0.06120.00430.15870.0290.11366.892937.961124.4382
131.01050.3843-0.24340.4058-0.3031.02990.03470.1164-0.2514-0.031-0.0663-0.08680.12440.1768-0.33180.00530.031-0.04690.20250.03070.11212.799825.480520.254
140.3247-0.1736-0.15060.4922-0.06660.12340.08590.1811-0.1566-0.136-0.05190.21950.0791-0.0502-0.5670.05420.0653-0.08760.19610.07950.26589.098817.755219.8089
150.006-0.00110.01710.0002-0.00310.0478-0.00680.0114-0.0446-0.01280.0016-0.02730.03080.0372-0.01090.33010.17280.0310.2208-0.02850.476310.01297.467617.1886
160.0502-0.0449-0.00390.11730.04040.0172-0.02660.0005-0.00770.0075-0.0323-0.07870.02650.0811-0.20740.12670.1489-0.04150.25960.17950.302416.71513.108928.0127
170.7918-0.10880.11320.4157-0.26990.17490.09130.0179-0.3147-0.2568-0.03210.01110.22980.0272-0.27110.11650.0155-0.00510.05280.05440.2309-9.001415.064715.1274
180.1115-0.04710.05740.1216-0.06360.06020.07050.0004-0.1021-0.0893-0.0589-0.0260.2060.0607-0.11290.18830.04830.01670.05880.08850.4469-1.12996.042522.221
190.0084-0.0276-0.01060.09010.03490.0134-0.0026-0.0147-0.00060.02780.028-0.02980.02770.01490.00060.34080.2205-0.0480.45830.12170.606712.81652.320632.8234
200.1908-0.05410.21590.0184-0.07990.35370.0462-0.0479-0.09710.004-0.0048-0.00180.10220.03890.00590.0830.0578-0.03110.28290.21980.19448.614417.244336.1477
210.66590.25650.25540.22350.21240.20280.01180.10590.0875-0.0655-0.02150.0468-0.0642-0.1017-0.28250.18080.1690.0170.49280.0630.1406-37.806943.46750.7581
220.0371-0.0326-0.01520.08490.00130.05430.0280.0084-0.0073-0.0086-0.0074-0.0345-0.0718-0.0648-0.04920.14660.12710.03970.07170.08180.1298-16.071944.782312.9984
230.0692-0.01930.07170.0556-0.03590.07960.0461-0.05930.01710.04960.0167-0.01680.02040.04410.00410.38560.08220.0330.4028-0.05180.1214-22.232747.579523.1498
240.0606-0.0130.05020.0658-0.03830.0550.02560.01610.072-0.0704-0.05030.0211-0.0632-0.0495-0.12380.37050.22960.08250.2704-0.00720.2293-29.111156.583412.7522
250.35950.12740.03690.26620.25010.2582-0.01340.08910.1651-0.0319-0.01940.0274-0.1945-0.15370.05910.09580.10740.02630.11640.08150.087-24.986543.57758.3214
260.0783-0.00810.13530.295-0.08780.25230.0357-0.06570.03550.0682-0.0040.0522-0.0919-0.0017-0.0590.15970.08240.05440.334-0.00180.1133-33.995445.836115.7961
270.0315-0.13450.10371.4721-0.23180.3876-0.0020.00770.0132-0.0419-0.0358-0.15960.00710.06890.09050.13410.05620.00660.1620.05780.0507-20.262338.02896.1022
280.0035-0.00250.00290.0018-0.00220.0026-0.03340.01780.00880.0251-0.0172-0.0305-0.04250.0317-0.00010.33350.0788-0.04620.4143-0.05390.5036-8.312221.93994.4629
290.38370.43630.09580.51170.1190.0311-0.05470.0583-0.2286-0.0505-0.0154-0.15480.30910.01570.02880.14640.00320.04890.11750.00230.0976-21.298925.20051.4859
300.1548-0.0091-0.13130.05260.02010.2838-0.05310.0104-0.01640.0087-0.01-0.01390.06240.0224-0.15690.07450.01920.00450.20050.04730.035-24.879334.90844.7789
310.05640.0284-0.05010.1054-0.01210.0464-0.03850.02480.07640.0095-0.0102-0.0827-0.01170.0888-0.00870.13090.0208-0.02620.37970.11920.2302-4.868235.97-6.0482
320.0397-0.0104-0.0460.0897-0.03530.10310.00750.0399-0.0144-0.0329-0.04350.01410.1102-0.1266-0.12390.09980.04030.01290.1827-0.02960.005-19.766330.7262-5.3401
331.1167-0.12220.05750.17420.2550.91610.0180.1530.1707-0.0513-0.0468-0.0153-0.2890.08040.3240.17690.0558-0.00680.15440.06480.0007-14.970443.2023-10.7687
340.1510.0426-0.15170.3087-0.10010.1655-0.0444-0.05020.0490.1926-0.0536-0.0892-0.14660.14540.47530.30620.1068-0.02510.23880.09340.0884-14.943550.904-7.0763
350.0762-0.07470.06070.0926-0.03690.0745-0.02990.04470.0628-0.0295-0.0191-0.0228-0.0270.0476-0.00210.55970.00510.08190.17530.09640.31-12.24461.2205-7.7019
360.05180.0707-0.00990.1066-0.04640.1056-0.01840.07010.0716-0.0394-0.0204-0.0099-0.0760.02360.09040.42310.19690.00570.36750.15860.1903-22.263655.5602-15.5349
370.5744-0.4698-0.37170.502-0.02381.1697-0.041-0.00050.34470.0261-0.0363-0.3596-0.40470.24250.13320.28760.01810.02290.12390.04650.238-12.22853.663611.4197
380.191-0.1990.08080.207-0.07390.1052-0.04420.03780.1802-0.0651-0.0347-0.023-0.106-0.0095-0.07680.45350.12510.080.10580.04990.3102-18.472962.66682.8175
390.06240.017-0.00930.01810.0050.0057-0.02430.02310.0584-0.0017-0.00150.0271-0.0404-0.0029-0.00540.70020.31520.07230.55310.20990.5483-27.483166.3499-12.2071
400.2049-0.07150.12490.0249-0.04580.11290.02170.0550.0603-0.0197-0.00480.0123-0.083-0.05870.07130.31040.2560.02790.42190.10280.155-31.239451.4264-8.3661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:19)A3 - 19
2X-RAY DIFFRACTION2(chain A and resid 20:41)A20 - 41
3X-RAY DIFFRACTION3(chain A and resid 42:47)A42 - 47
4X-RAY DIFFRACTION4(chain A and resid 48:61)A48 - 61
5X-RAY DIFFRACTION5(chain A and resid 62:81)A62 - 81
6X-RAY DIFFRACTION6(chain A and resid 82:87)A82 - 87
7X-RAY DIFFRACTION7(chain A and resid 88:109)A88 - 109
8X-RAY DIFFRACTION8(chain A and resid 110:114)A110 - 114
9X-RAY DIFFRACTION9(chain A and resid 115:131)A115 - 131
10X-RAY DIFFRACTION10(chain A and resid 132:149)A132 - 149
11X-RAY DIFFRACTION11(chain A and resid 150:155)A150 - 155
12X-RAY DIFFRACTION12(chain A and resid 156:175)A156 - 175
13X-RAY DIFFRACTION13(chain A and resid 176:217)A176 - 217
14X-RAY DIFFRACTION14(chain A and resid 218:240)A218 - 240
15X-RAY DIFFRACTION15(chain A and resid 241:248)A241 - 248
16X-RAY DIFFRACTION16(chain A and resid 249:262)A249 - 262
17X-RAY DIFFRACTION17(chain A and resid 263:282)A263 - 282
18X-RAY DIFFRACTION18(chain A and resid 283:302)A283 - 302
19X-RAY DIFFRACTION19(chain A and resid 303:310)A303 - 310
20X-RAY DIFFRACTION20(chain A and resid 311:325)A311 - 325
21X-RAY DIFFRACTION21(chain B and resid 3:19)B3 - 19
22X-RAY DIFFRACTION22(chain B and resid 20:41)B20 - 41
23X-RAY DIFFRACTION23(chain B and resid 42:47)B42 - 47
24X-RAY DIFFRACTION24(chain B and resid 48:61)B48 - 61
25X-RAY DIFFRACTION25(chain B and resid 62:81)B62 - 81
26X-RAY DIFFRACTION26(chain B and resid 82:87)B82 - 87
27X-RAY DIFFRACTION27(chain B and resid 88:109)B88 - 109
28X-RAY DIFFRACTION28(chain B and resid 110:114)B110 - 114
29X-RAY DIFFRACTION29(chain B and resid 115:131)B115 - 131
30X-RAY DIFFRACTION30(chain B and resid 132:149)B132 - 149
31X-RAY DIFFRACTION31(chain B and resid 150:155)B150 - 155
32X-RAY DIFFRACTION32(chain B and resid 156:175)B156 - 175
33X-RAY DIFFRACTION33(chain B and resid 176:217)B176 - 217
34X-RAY DIFFRACTION34(chain B and resid 218:240)B218 - 240
35X-RAY DIFFRACTION35(chain B and resid 241:248)B241 - 248
36X-RAY DIFFRACTION36(chain B and resid 249:262)B249 - 262
37X-RAY DIFFRACTION37(chain B and resid 263:282)B263 - 282
38X-RAY DIFFRACTION38(chain B and resid 283:302)B283 - 302
39X-RAY DIFFRACTION39(chain B and resid 303:310)B303 - 310
40X-RAY DIFFRACTION40(chain B and resid 311:325)B311 - 325

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