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- PDB-3czp: Crystal structure of putative polyphosphate kinase 2 from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 3czp
TitleCrystal structure of putative polyphosphate kinase 2 from Pseudomonas aeruginosa PA01
ComponentsPutative polyphosphate kinase 2
KeywordsTRANSFERASE / PPK2 / polyphosphate kinase / kinase / MCSG / PSI-2 / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


AMP-polyphosphate phosphotransferase / polyphosphate:AMP phosphotransferase activity / polyphosphate metabolic process / kinase activity / identical protein binding
Similarity search - Function
Polyphosphate:AMP phosphotransferase / Polyphosphate kinase-2-related / Polyphosphate kinase 2 (PPK2) / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / MALONATE ION / Polyphosphate:AMP phosphotransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsNocek, B. / Evdokimova, E. / Osipiuk, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria.
Authors: Nocek, B. / Kochinyan, S. / Proudfoot, M. / Brown, G. / Evdokimova, E. / Osipiuk, J. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Yakunin, A.F.
History
DepositionApr 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative polyphosphate kinase 2
B: Putative polyphosphate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,00815
Polymers118,0562
Non-polymers95213
Water12,034668
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-5.9 kcal/mol
Surface area41630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.089, 100.735, 120.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative polyphosphate kinase 2 /


Mass: 59028.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3455 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYF1

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Non-polymers , 5 types, 681 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 668 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% Tacsimate, 10% PEG MME 5000, 0.1M Hepes pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2006 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 79999 / Num. obs: 76187 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / % possible all: 72.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
ARP/wARPmodel building
Cootmodel building
MLPHAREphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.068 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / ESU R: 0.169 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 3811 5 %RANDOM
Rwork0.17349 ---
obs0.17625 72297 94.99 %-
all-76108 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å20 Å20 Å2
2--2.64 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7692 0 63 668 8423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0227986
X-RAY DIFFRACTIONr_bond_other_d0.0030.025747
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.95110769
X-RAY DIFFRACTIONr_angle_other_deg0.981313755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30122.759435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.501151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5571595
X-RAY DIFFRACTIONr_chiral_restr0.0980.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028885
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021821
X-RAY DIFFRACTIONr_nbd_refined0.2160.21608
X-RAY DIFFRACTIONr_nbd_other0.2030.26081
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23741
X-RAY DIFFRACTIONr_nbtor_other0.0860.24156
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2463
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1071.55754
X-RAY DIFFRACTIONr_mcbond_other0.2521.51876
X-RAY DIFFRACTIONr_mcangle_it1.32127437
X-RAY DIFFRACTIONr_scbond_it2.26733915
X-RAY DIFFRACTIONr_scangle_it3.1774.53325
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 212 -
Rwork0.219 4007 -
obs--72.37 %
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)
110.7735-3.33311.676713.88232.966639.22820.07211.10380.00840.58230.4485-1.458-0.64144.7543-0.5206-0.1567-0.00460.00910.5433-0.0281-0.023343.49747.118-12.848
23.7915-1.72641.39911.1845-1.21382.2594-0.0226-0.43840.12670.10720.0360.0063-0.18490.1164-0.01340.0671-0.0305-0.04840.0933-0.001-0.017628.11158.1314.812
32.9567-0.446-0.87470.69440.333.1335-0.0717-0.0089-0.10790.0675-0.01930.03730.22850.19210.0910.0454-0.00010.00150.0592-0.00340.012922.12349.23-3.928
43.23762.59962.50943.31152.11573.13140.20870.1835-0.28040.1132-0.027-0.23150.2781-0.0735-0.18180.06960.0143-0.04070.06920.00840.05659.79549.369-17.438
51.7736-0.6958-0.88981.49890.50431.4288-0.00450.261-0.126-0.035-0.08850.03730.0820.03970.09310.020.0058-0.00570.1362-0.02450.024222.78549.258-22.574
62.5347-2.81480.76283.6533-0.7461.634-0.0291-0.05110.1133-0.03830.05-0.0203-0.11250.3281-0.02090.0034-0.0101-0.01090.11010.01470.02227.35255.01-12.71
716.4631-0.13314.52948.2097.010420.53190.1305-0.6678-1.58970.12350.064-0.02682.4409-0.2844-0.19450.36490.1489-0.00850.05490.08130.004134.64133.754-14.926
80.7824-0.4651-0.26941.19070.80012.97160.0136-0.02490.03220.0229-0.0303-0.13650.07820.28770.0167-0.0371-0.0049-0.00050.19030.0199-0.008433.39151.511-12.553
93.12210.11614.32620.945-0.55017.2567-0.53561.20850.84520.2364-0.1543-0.1749-2.12731.77480.68990.27970.10620.10850.19370.28240.259713.3776.321-28.675
102.87241.76831.09469.0209-1.60842.14520.0250.80990.2625-0.91110.11771.1506-0.1094-0.3893-0.14270.1010.2294-0.1360.3342-0.0006-0.0109-13.77266.816-47.179
112.6957-0.5979-0.14671.8150.33391.72650.0510.3655-0.2122-0.0943-0.03650.14920.1144-0.137-0.01450.02820.0638-0.04020.109-0.04-0.0394-4.06953.969-36.143
123.86271.4369-0.49775.9896-1.44693.38290.11470.1471-0.0035-0.0473-0.120.44950.0316-0.47750.00530.00190.0888-0.02740.1451-0.05490.0105-12.4957.472-31.232
133.17750.20120.43280.64411.01151.5928-0.0421-0.21350.1586-0.0332-0.02210.0898-0.1612-0.00780.06420.09730.0604-0.01780.06210.00820.02553.73763.621-16.772
145.5376-0.36671.05766.1692.89114.92730.0902-0.1033-0.18450.2089-0.01130.03210.1537-0.2708-0.07890.01970.02010.0060.08840.002-0.0297-1.41655.604-26.478
156.3968-0.32632.26941.56981.68685.3092-0.1011-0.00350.71080.122-0.07790.0012-0.4740.03180.17910.11750.046-0.02290.02140.07450.0978.77374.361-24.677
160.96970.08740.45951.1186-0.0720.63140.1090.33060.1169-0.0733-0.1243-0.1566-0.02360.08130.01530.07130.08240.0180.11180.0414-0.00286.12664.042-32.952
1744.5157-6.7933-6.676715.581113.869121.24540.1523-1.07121.66860.33710.0920.4237-0.2927-1.1983-0.2443-0.03230.21510.064-0.04610.18980.1389-14.92581.687-32.842
1819.6196-1.0042-7.53639.6006-6.17237.39870.7235-1.95550.93531.1489-0.75690.1733-1.0103-0.08590.03330.46910.0606-0.00220.4759-0.00280.4517-13.7481.16-24.844
193.991-0.64021.26032.4677-0.32892.43640.02810.61020.5166-0.2328-0.1851-0.0173-0.33390.10550.15690.07320.1139-0.01140.08690.1381-0.03551.11572.023-38.043
208.603-5.3649-5.388314.56326.95256.22580.0630.2844-0.0872-0.7728-0.0078-0.1774-0.13520.1272-0.05520.0470.0559-0.03730.1997-0.0392-0.1124-0.56552.527-43.427
218.42922.49122.442211.81280.49076.4038-0.3650.45530.1711-0.37980.41140.2465-0.0199-0.9045-0.0464-0.2039-0.0302-0.18280.23050.0008-0.2631-37.10655.919-28.987
2211.27933.62758.25064.93653.571213.101-0.38680.2960.5444-0.41290.19060.1507-0.72170.06620.1962-0.00080.0755-0.0550.0911-0.02880.0008-21.2767.857-19.48
233.65760.97290.96973.15870.80851.860.10410.0605-0.033-0.26580.110.21020.1106-0.3911-0.21410.01670.0115-0.09330.210.02180.0311-20.78253.8-21.76
248.2125-10.28034.313414.3038-5.78242.36770.35240.102-0.3314-0.1367-0.06680.60570.1026-0.0691-0.28560.1025-0.0098-0.05660.2047-0.02880.0175-7.68545.665-17.933
251.1954-0.72381.02781.3402-0.88831.11010.1424-0.1749-0.0508-0.30840.01640.11340.1399-0.1537-0.15880.0196-0.0203-0.05480.2178-0.0017-0.0045-10.71348.158-11.713
2614.4099-0.0531-4.574119.0536-3.9482.277-0.50480.6997-1.3482-0.55780.63540.08790.99580.3858-0.13060.2044-0.14-0.17990.21040.06550.1548-18.65330.735-12.151
272.7471-0.08441.64871.83320.61914.160.2233-0.5712-0.4204-0.0391-0.00830.29740.4455-0.5807-0.215-0.0554-0.1153-0.08440.29170.12140.0571-22.8144.5-8.089
284.6129-0.29313.08386.85240.548110.76350.5974-0.2139-1.3228-0.3565-0.00650.63991.4443-0.9739-0.5909-0.0243-0.2381-0.30360.2070.17610.3579-29.78135.31-16.449
292.97560.6741.26442.6463-0.80881.06180.1539-0.3459-0.1395-0.21590.01730.39730.046-0.6257-0.1712-0.0507-0.0385-0.11060.36810.06590.0119-30.34353.568-17.233
304.1879-1.09125.44060.2849-1.335818.6523-1.0415-1.2434-0.29960.91380.72620.5885-2.2546-1.79170.31530.3374-0.053-0.04060.4408-0.19180.2956-12.65457.88915.15
311.19450.13160.28442.13161.73654.88360.0099-0.1259-0.1390.05530.16-0.1550.31980.1458-0.16990.0395-0.0096-0.01120.06220.0075-0.03415.06839.63220.074
320.9636-0.47850.69855.35332.44013.55260.0922-0.144-0.1707-0.12620.0055-0.04780.3512-0.3204-0.09770.0705-0.09760.00670.07470.01980.02646.70140.1845.759
332.5288-0.880.10273.79851.94074.44050.0562-0.1556-0.004-0.19950.1346-0.17320.00460.2323-0.19080.0502-0.0430.03640.0779-0.00690.014915.52345.4835.301
341.4554-2.31881.42753.7277-2.20671.5377-0.04710.01530.2884-0.0443-0.1806-0.1973-0.0865-0.05980.22770.0358-0.0049-0.01880.2412-0.0217-0.0031-2.08358.235-2.081
352.775-1.09880.05042.44881.46074.90.10480.23550.0493-0.2192-0.0207-0.12060.036-0.2042-0.08410.0358-0.06430.01080.10270.03-0.00242.76346.91-0.449
361.16080.07560.95870.87530.07643.1715-0.0547-0.24260.0260.01420.04090.0747-0.0119-0.67340.0138-0.0618-0.010.00430.23040.0065-0.0304-4.02352.18111.585
3715.03695.9124-6.85648.1338-2.483422.1080.23010.27690.37280.18830.1695-0.3237-0.84510.8866-0.39960.11740.005-0.08010.0707-0.032-0.012718.81164.81819.979
3840.8258-3.9667-26.6791.25295.50638.06320.03641.94481.212-0.40720.25550.1609-0.2244-0.9173-0.29190.10840.07-0.05390.1910.11340.019312.98466.81613.806
398.86064.6072.18775.33192.06563.7107-0.1827-0.34750.76030.22630.01250.3765-0.2148-0.50460.1702-0.0180.1202-0.02130.29-0.0286-0.0547-2.28959.97320.953
400.8255-0.41510.48571.17510.2592.89280.0442-0.2721-0.20560.12560.11070.0660.4189-0.3825-0.15490.0594-0.09110.00130.13340.02990.01644.36639.20814.903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 84 - 10
2X-RAY DIFFRACTION2AA9 - 4011 - 42
3X-RAY DIFFRACTION3AA41 - 7543 - 77
4X-RAY DIFFRACTION4AA76 - 9978 - 101
5X-RAY DIFFRACTION5AA100 - 139102 - 141
6X-RAY DIFFRACTION6AA140 - 155142 - 157
7X-RAY DIFFRACTION7AA156 - 185158 - 187
8X-RAY DIFFRACTION8AA186 - 232188 - 234
9X-RAY DIFFRACTION9AA233 - 261235 - 263
10X-RAY DIFFRACTION10AA262 - 282264 - 284
11X-RAY DIFFRACTION11AA283 - 310285 - 312
12X-RAY DIFFRACTION12AA311 - 328313 - 330
13X-RAY DIFFRACTION13AA329 - 349331 - 351
14X-RAY DIFFRACTION14AA350 - 363352 - 365
15X-RAY DIFFRACTION15AA364 - 384366 - 386
16X-RAY DIFFRACTION16AA385 - 414387 - 416
17X-RAY DIFFRACTION17AA415 - 424417 - 426
18X-RAY DIFFRACTION18AA425 - 442427 - 444
19X-RAY DIFFRACTION19AA443 - 480445 - 482
20X-RAY DIFFRACTION20AA481 - 496483 - 498
21X-RAY DIFFRACTION21BB6 - 218 - 23
22X-RAY DIFFRACTION22BB22 - 3824 - 40
23X-RAY DIFFRACTION23BB39 - 6841 - 70
24X-RAY DIFFRACTION24BB69 - 8371 - 85
25X-RAY DIFFRACTION25BB84 - 11086 - 112
26X-RAY DIFFRACTION26BB111 - 122113 - 124
27X-RAY DIFFRACTION27BB123 - 157125 - 159
28X-RAY DIFFRACTION28BB158 - 202160 - 204
29X-RAY DIFFRACTION29BB203 - 234205 - 236
30X-RAY DIFFRACTION30BB235 - 260237 - 262
31X-RAY DIFFRACTION31BB261 - 289263 - 291
32X-RAY DIFFRACTION32BB290 - 310292 - 312
33X-RAY DIFFRACTION33BB311 - 328313 - 330
34X-RAY DIFFRACTION34BB329 - 346331 - 348
35X-RAY DIFFRACTION35BB347 - 363349 - 365
36X-RAY DIFFRACTION36BB364 - 419366 - 421
37X-RAY DIFFRACTION37BB420 - 428422 - 430
38X-RAY DIFFRACTION38BB429 - 437431 - 439
39X-RAY DIFFRACTION39BB438 - 456440 - 458
40X-RAY DIFFRACTION40BB457 - 496459 - 498

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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

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