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- PDB-3ty5: Crystal Structure of C. thermocellum PNKP Ligase domain in comple... -

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Basic information

Entry
Database: PDB / ID: 3ty5
TitleCrystal Structure of C. thermocellum PNKP Ligase domain in complex with ATP
ComponentsPolynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
KeywordsTRANSFERASE / DNA ligase/mRNA capping enzyme / RNA Ligase / Adenylyltransferase / HEN1
Function / homology
Function and homology information


hydrolase activity / carbohydrate metabolic process / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Helix Hairpins - #1010 / : / Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / AAA domain / DNA ligase/mRNA capping enzyme / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type ...Helix Hairpins - #1010 / : / Polynucleotide kinase-phosphatase, bacterial / PrpE-like, metallophosphatase domain / Polynucleotide kinase-phosphatase, ligase domain / PNKP adenylyltransferase domain, ligase domain / AAA domain / DNA ligase/mRNA capping enzyme / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Helix Hairpins / Metallo-dependent phosphatase-like / D-amino Acid Aminotransferase; Chain A, domain 1 / Helix non-globular / Special / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / TRIETHYLENE GLYCOL / Metallophosphoesterase
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsSmith, P. / Wang, L. / Shuman, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: The adenylyltransferase domain of bacterial Pnkp defines a unique RNA ligase family.
Authors: Smith, P. / Wang, L.K. / Nair, P.A. / Shuman, S.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
B: Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0355
Polymers94,9512
Non-polymers1,0853
Water3,837213
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-22 kcal/mol
Surface area33410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.989, 94.381, 75.314
Angle α, β, γ (deg.)90.00, 93.51, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE DIMERIC CONFIGURATION SEEN HERE IS NOT RELATED BY PROPER SYMMETRY AND IS UNLIKELY TO REPRESENT THE CONFIGURATION PRESENT IN THE HEN1/PNKP HETEROTETRAMER

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Components

#1: Protein Polynucleotide 2',3'-cyclic phosphate phosphodiesterase / polynucleotide 5'-hydroxyl-kinase / polynucleotide 3'-phosphatase


Mass: 47475.262 Da / Num. of mol.: 2 / Fragment: Nucleotide Ligase / Mutation: E529G
Source method: isolated from a genetically manipulated source
Details: See Citation / Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / Gene: Cthe_2768 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3DJ38, RNA ligase (ATP)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2-0.25 M di-ammoinium tartrate and 20% (w/v) Polyethylene Glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2011 / Details: See Beamline Documentation
RadiationMonochromator: See Beamline Documentation / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 30993 / % possible obs: 99.1 % / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→44.33 Å / SU ML: 0.31 / σ(F): 1.37 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1728 5.1 %Random
Rwork0.1776 ---
obs0.18 33879 96.7 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.389 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.1058 Å20 Å27.7062 Å2
2--0.7172 Å2-0 Å2
3----4.823 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 68 213 6381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066300
X-RAY DIFFRACTIONf_angle_d1.1028514
X-RAY DIFFRACTIONf_dihedral_angle_d14.132352
X-RAY DIFFRACTIONf_chiral_restr0.06919
X-RAY DIFFRACTIONf_plane_restr0.0031084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.47080.33441100.27552078X-RAY DIFFRACTION76
2.4708-2.55050.35191290.282400X-RAY DIFFRACTION87
2.5505-2.64170.36871200.27582722X-RAY DIFFRACTION98
2.6417-2.74740.32441550.24392755X-RAY DIFFRACTION100
2.7474-2.87240.29561620.23222735X-RAY DIFFRACTION100
2.8724-3.02380.28151470.21442778X-RAY DIFFRACTION100
3.0238-3.21320.27391380.20112773X-RAY DIFFRACTION100
3.2132-3.46130.21531710.18572742X-RAY DIFFRACTION100
3.4613-3.80940.22341430.15982773X-RAY DIFFRACTION100
3.8094-4.36020.17761660.14052760X-RAY DIFFRACTION100
4.3602-5.49180.16521490.13582789X-RAY DIFFRACTION100
5.4918-44.33770.20421380.16482846X-RAY DIFFRACTION100
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)
11.4319-0.33550.51474.5032-1.05270.38830.12730.0283-0.0699-0.05480.18480.58340.4470.1166-0.25731.69660.31680.10131.20370.19121.361322.44518.22339.3234
21.19480.6804-0.97861.5522-0.68351.4997-0.1327-0.0253-0.1457-0.04870.3853-0.04920.2563-0.1893-0.05010.4155-0.0476-0.00690.33180.06080.363723.363113.835624.9792
30.3723-0.10010.22980.07770.01640.31640.0279-0.1767-0.27630.1966-0.0484-0.02670.2671-0.0207-0.20350.37620.08940.03580.26410.66350.634822.54780.983241.3919
41.44890.6413-0.46260.41610.11110.9335-0.0879-0.2589-0.351-0.14890.14180.0129-0.10270.1725-0.03830.32010.0414-0.00370.23860.06480.308117.808616.907834.4686
51.8544-0.1867-0.89650.45250.99362.29350.31580.04870.4376-0.4011-0.0936-0.2852-0.7090.1019-0.20590.4423-0.08570.0570.3020.00490.506431.541335.857920.6651
61.01910.14220.15391.6698-0.03480.67160.20950.33880.2971-0.7384-0.19170.3035-0.30680.1613-0.0170.34530.05070.00370.2223-0.01120.294720.745427.414617.9997
70.61130.566-0.09561.2814-0.40850.32480.2358-0.21830.36970.21940.02560.1873-0.65530.12750.60010.4678-0.10080.04080.1951-0.09140.303523.410833.324229.4635
80.967-0.31090.43510.93940.52980.74390.4619-0.12390.17690.2104-0.1205-0.048-0.129-0.2422-0.10830.48370.06930.18080.40850.04640.41242.356223.80337.2623
90.9171-0.11030.98780.0339-0.15751.34340.3388-0.2136-0.24970.08570.42610.43270.5148-0.4876-0.3320.6043-0.1507-0.12570.44680.06960.4938-2.79357.779420.2972
103.28182.14110.30413.20712.88754.14660.14230.05810.13750.3537-0.3708-0.00230.4332-0.34490.17150.685-0.2650.10250.91180.23220.7067-25.01438.16846.916
111.6519-2.0489-0.03432.56580.12571.6509-0.0328-0.11940.15070.19540.0328-0.48350.34510.36080.05440.6498-0.0044-0.05020.57970.10580.5416-11.182812.16577.0158
120.8837-0.02-1.16253.43530.83961.7197-0.10380.43340.10790.06740.10620.7267-0.0646-0.111-0.0140.36430.0581-0.00670.45450.02280.41691.563118.122419.671
132.40.7686-0.06160.4928-0.05320.63190.1951-0.30030.16190.5004-0.03450.0119-0.35210.1338-0.07080.387-0.0561-0.02590.3115-0.01340.300824.49125.426331.9947
141.1962-0.5013-0.93952.48510.46450.75050.2337-0.48690.19810.6371-0.05340.2697-0.42680.1707-0.09690.6957-0.13580.01790.5305-0.05220.396824.778329.784639.3936
151.1397-0.68670.23561.1460.24040.2576-0.1011-0.9127-0.15040.75390.11070.1061-0.499-0.3937-0.00270.55750.0503-0.0860.60780.17170.370417.148510.796346.4738
160.6292-0.4718-0.68641.255-0.30521.71-0.2481-0.48540.18420.0067-0.0708-0.529-0.09210.6910.22250.33860.0249-0.0610.53050.21360.481829.82328.283535.7966
173.78281.15672.16351.90060.40731.2807-0.0312-0.7665-0.25010.0668-0.13490.26080.1037-0.24610.01620.3814-0.0254-0.02490.45190.12430.51396.66234.303933.0787
183.6168-0.4785-1.62570.07160.30011.6323-0.1403-0.0422-0.95680.2261-0.1755-0.0320.7827-0.15010.14450.9709-0.3101-0.26940.49430.13391.01724.9295-6.191832.5853
190.0813-0.1010.13640.2891-0.39251.6906-0.166-0.1187-0.416-0.1372-0.0341-0.25250.33110.40120.14450.28530.0080.06740.26420.07840.461331.29211.438121.8752
202.73731.283-1.07342.0252-1.29340.8514-0.1120.4705-0.1582-0.45080.1632-0.13520.6359-0.16740.01720.3656-0.0742-0.01940.2733-0.13560.37221.30436.844618.5677
211.7984-1.7358-1.18382.14680.90361.04590.3599-0.85920.02590.0891-0.3122-0.9401-0.30330.4633-0.07370.4308-0.10420.08750.65330.17290.7101-17.030821.884310.0091
221.3502-0.0002-0.84880.2486-0.12711.2915-0.08920.13-0.0352-0.1276-0.0367-0.08110.3599-0.07090.03750.40290.01770.12010.39210.07280.4102-11.615317.7365-10.1863
231.4057-0.4998-0.73051.34340.01621.1281-0.2630.1814-0.1105-0.4629-0.3679-0.3420.61310.37120.12570.4130.08880.08250.39590.05730.3074-0.742116.7233-26.684
241.02210.5339-0.61750.6268-0.3881.37430.0994-0.0396-0.21720.1929-0.0184-0.073-0.4030.2233-0.04460.38020.05350.02430.47430.02550.298-9.851327.4673-14.1846
250.6062-0.7581-0.02041.28750.37542.34040.29710.1601-0.06180.2485-0.04880.5094-0.196-0.7547-0.04430.33380.00920.14150.51940.06070.3936-31.01727.5953-0.9825
261.0994-0.0947-0.01453.28880.42811.60430.0420.1297-0.12180.0797-0.1091-0.5552-0.60440.01780.01960.5117-0.03790.01280.320.02130.3856-16.289828.5022.8741
272.9879-1.39672.37260.6532-1.07184.73040.124-0.19640.50690.142-0.149-0.07-0.7353-0.4412-0.05010.57690.12430.14570.4704-0.01160.5195-25.110638.28-6.1833
281.0481-0.0657-0.75671.1195-0.35062.16410.06860.0864-0.1107-0.01880.02870.2291-0.3521-0.6157-0.09380.30570.06280.04230.42120.03460.3596-19.396130.0158-7.9601
291.26960.2391-0.04872.84111.13090.4633-0.02310.61360.0647-0.41770.2512-0.0404-0.292-0.1555-0.07050.36520.0584-0.08250.44070.05770.28289.098518.251317.0663
303.61060.8553-1.2730.47230.24635.6387-0.11320.5615-1.329-0.85550.0582-0.11940.8068-0.1230.0430.8519-0.0407-0.14380.4829-0.16980.80964.55490.615614.2651
311.5744-0.057-0.24492.7227-0.39230.0982-0.1670.6141-0.0247-0.81810.04980.05340.36340.41960.03810.74380.0186-0.13870.96710.08410.52625.962618.1442.9518
321.92510.1412-1.63862.69561.33523.21790.0476-0.64490.48150.7214-0.15820.0420.06720.5443-0.01480.7264-0.181-0.06920.6233-0.08250.5525-0.201834.2676-3.8675
332.87710.5510.05011.67010.48362.80530.28270.29190.50210.0621-0.23490.1517-0.3101-0.5016-0.05220.37640.02170.04310.47170.07990.3801-20.1130.44-11.1952
341.6818-0.06020.23710.7921.021.42620.38280.5910.0645-0.35550.0389-0.0266-0.3574-0.3394-0.1650.50430.08250.00510.66010.0430.3965-22.155628.1427-21.3755
352.0184-0.41750.73281.854-0.64460.98420.35490.34510.44670.1369-0.1311-0.0951-0.20140.2062-0.14580.52560.12830.15490.43820.05970.4691-16.333439.0284-15.1444
361.61050.18130.00731.2490.04250.38390.07110.33710.3288-0.2855-0.1093-0.1083-0.44130.0081-0.00490.41910.04530.03720.48910.03690.342-2.481427.0236-26.7149
371.34780.0163-0.62331.9103-0.31092.1603-0.2290.1027-0.0089-0.3418-0.1874-0.18030.2837-0.01680.20580.3731-0.05450.07350.41420.00830.3389-4.443617.7986-18.694
380.4519-0.8752-0.78043.29750.98721.7230.0369-0.66690.2962-0.09820.2847-1.22280.28680.6152-0.09280.50910.19230.15290.80190.12530.994610.638410.0812-14.1922
390.8370.9202-0.49351.17-0.56831.5575-0.14450.118-0.4745-0.1115-0.30260.15610.6014-0.35440.15470.4107-0.13670.01570.3906-0.0230.3714-20.274511.0624-8.5239
401.6038-0.4356-0.48560.61040.09930.80440.04010.1891-0.0945-0.1212-0.3715-0.07250.04780.43760.13410.82070.18710.08420.90530.34760.7074-0.907712.3381-5.8194
410.1379-0.1586-0.13180.19940.14680.1281-0.00140.0218-0.1388-0.0659-0.26280.1244-0.006-0.01280.09951.2056-0.1266-0.15870.61480.24341.039817.573614.32629.619
420.23230.0717-0.02850.3801-0.05740.15840.13530.0129-0.06530.0407-0.0263-0.0643-0.06780.0066-0.06251.06950.16970.18641.1764-0.18541.1843-7.53722.3484-11.5365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 477:481)
2X-RAY DIFFRACTION2(chain A and resid 482:504)
3X-RAY DIFFRACTION3(chain A and resid 505:525)
4X-RAY DIFFRACTION4(chain A and resid 526:538)
5X-RAY DIFFRACTION5(chain A and resid 539:553)
6X-RAY DIFFRACTION6(chain A and resid 554:572)
7X-RAY DIFFRACTION7(chain A and resid 573:611)
8X-RAY DIFFRACTION8(chain A and resid 612:627)
9X-RAY DIFFRACTION9(chain A and resid 628:647)
10X-RAY DIFFRACTION10(chain A and resid 648:664)
11X-RAY DIFFRACTION11(chain A and resid 665:677)
12X-RAY DIFFRACTION12(chain A and resid 678:691)
13X-RAY DIFFRACTION13(chain A and resid 692:720)
14X-RAY DIFFRACTION14(chain A and resid 721:737)
15X-RAY DIFFRACTION15(chain A and resid 738:770)
16X-RAY DIFFRACTION16(chain A and resid 771:793)
17X-RAY DIFFRACTION17(chain A and resid 794:805)
18X-RAY DIFFRACTION18(chain A and resid 806:814)
19X-RAY DIFFRACTION19(chain A and resid 815:855)
20X-RAY DIFFRACTION20(chain A and resid 856:870)
21X-RAY DIFFRACTION21(chain B and resid 477:483)
22X-RAY DIFFRACTION22(chain B and resid 484:504)
23X-RAY DIFFRACTION23(chain B and resid 505:525)
24X-RAY DIFFRACTION24(chain B and resid 526:539)
25X-RAY DIFFRACTION25(chain B and resid 540:563)
26X-RAY DIFFRACTION26(chain B and resid 564:576)
27X-RAY DIFFRACTION27(chain B and resid 577:590)
28X-RAY DIFFRACTION28(chain B and resid 591:621)
29X-RAY DIFFRACTION29(chain B and resid 622:643)
30X-RAY DIFFRACTION30(chain B and resid 644:669)
31X-RAY DIFFRACTION31(chain B and resid 670:680)
32X-RAY DIFFRACTION32(chain B and resid 681:695)
33X-RAY DIFFRACTION33(chain B and resid 696:712)
34X-RAY DIFFRACTION34(chain B and resid 713:731)
35X-RAY DIFFRACTION35(chain B and resid 732:741)
36X-RAY DIFFRACTION36(chain B and resid 742:775)
37X-RAY DIFFRACTION37(chain B and resid 776:805)
38X-RAY DIFFRACTION38(chain B and resid 806:820)
39X-RAY DIFFRACTION39(chain B and resid 821:862)
40X-RAY DIFFRACTION40(chain B and resid 863:870)
41X-RAY DIFFRACTION41(chain A and resid 1001)
42X-RAY DIFFRACTION42(chain B and resid 1001)

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