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- PDB-4h9u: Structure of Geobacillus kaustophilus lactonase, wild-type with Zn2+ -

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Basic information

Entry
Database: PDB / ID: 4h9u
TitleStructure of Geobacillus kaustophilus lactonase, wild-type 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: 2.099 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)74,0368
Polymers73,7602
Non-polymers2776
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-136 kcal/mol
Surface area23360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.340, 157.122, 49.936
Angle α, β, γ (deg.)90.000, 116.180, 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: (0.270367, -0.712584, 0.6474), (-0.712294, -0.600454, -0.363444), (0.647718, -0.362876, -0.669912)
Vector: 7.56682, 56.7556, 47.446301)

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Components

#1: Protein Phosphotriesterase


Mass: 36879.922 Da / Num. of mol.: 2
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.: 273 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
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: 2.099→30 Å / Num. all: 37427 / Num. obs: 37427 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Χ2: 0.875 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1430.41817860.774192.5
2.14-2.183.10.3818240.811195.9
2.18-2.223.30.37718210.784197.4
2.22-2.263.30.35718711.57196.4
2.26-2.313.60.32118380.845198
2.31-2.373.70.21819020.796198.1
2.37-2.423.70.19418330.815198.4
2.42-2.493.80.15918950.785198.5
2.49-2.563.80.13218630.788198.2
2.56-2.653.80.11318870.775198.8
2.65-2.743.80.11818611.08198.5
2.74-2.853.80.0918990.853198.9
2.85-2.983.80.07118860.834198.6
2.98-3.143.80.06118840.832199
3.14-3.333.80.05418860.814199.2
3.33-3.593.80.05418950.978199.2
3.59-3.953.70.05419071.088199.1
3.95-4.523.70.04818780.9199.2
4.52-5.693.60.04518880.726197.8
5.69-303.80.04719230.698198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.56 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.89 Å
Translation3.5 Å19.89 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: 2.099→19.889 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 0 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 1695 5.01 %random
Rwork0.1725 ---
all0.1747 33812 --
obs0.1747 33812 88.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.337 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso max: 121.37 Å2 / Biso mean: 32.5037 Å2 / Biso min: 4.27 Å2
Baniso -1Baniso -2Baniso -3
1-4.4845 Å20 Å20.1237 Å2
2--0.651 Å2-0 Å2
3---1.3652 Å2
Refinement stepCycle: LAST / Resolution: 2.099→19.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 6 273 5365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125204
X-RAY DIFFRACTIONf_angle_d1.2887042
X-RAY DIFFRACTIONf_chiral_restr0.084758
X-RAY DIFFRACTIONf_plane_restr0.006930
X-RAY DIFFRACTIONf_dihedral_angle_d14.7521930
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2333X-RAY DIFFRACTIONPOSITIONAL0.062
12B2333X-RAY DIFFRACTIONPOSITIONAL0.062
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.099-2.16070.2661540.20421123117737
2.1607-2.23030.2639820.21451784186659
2.2303-2.30990.3051220.23592447256982
2.3099-2.40230.23611720.19832910308298
2.4023-2.51140.25881600.18972983314398
2.5114-2.64350.24541430.18572969311299
2.6435-2.80870.22571690.1942952312199
2.8087-3.02490.24881640.19642972313699
3.0249-3.3280.22491410.18623003314499
3.328-3.80670.20211510.16482991314299
3.8067-4.7850.18211570.1313001315899
4.785-19.88950.18451800.15052982316299
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)
10.00780.0112-0.00530.0181-0.00710.0018-0.0010.0091-0.0055-0.00680.0351-0.03230.00270.02960.04840.15360.04160.07190.1634-0.12110.290315.13050.65059.8795
20.04890.002-0.00740.01220.01390.02730.0155-0.0253-0.0240.1809-0.0197-0.0419-0.00010.021-0.00090.2042-0.052-0.00340.0679-0.02440.06164.51815.42527.1678
30-0-00.00010.00010.00020.0019-0.0009-0.001-0.0073-0.001-00.0065-0.010600.48120.0766-0.08070.27390.06480.19210.89639.871435.7147
40.0346-0.00270.01590.0034-0.010.0302-0.0055-0.0348-0.00780.0330.0152-0.0078-0.0036-0.00860.020.51920.0318-0.11860.18470.05870.19066.0543-2.035327.2893
50.0405-0.0056-0.01070.04010.00560.00760.0629-0.0811-0.02910.04170.0117-0.04150.06380.0680.04640.1020.0007-0.02340.136-0.02170.09619.209310.052620.0294
60.01230.0004-0.00510.0003-0.00020.0026-0.0083-0.00520.01530.01540.0158-0.0263-0.01940.00730.04670.33080.0738-0.18720.27330.01840.371416.96723.053625.3905
70.1236-0.06640.0440.04420.00780.18870.0687-0.006-0.00390.03470.09470.0434-0.04510.0420.14230.0745-0.0160.02850.08140.00020.0856.717618.545217.5964
80.0001-0.0001-00.000200.00010.0053-0.0123-0.0095-0.0020.0026-0.0034-0.0122-0.00800.2548-0.08020.08360.1818-0.04560.17378.923436.179813.4224
90.00930.0118-0.0060.016-0.01510.022-0.01040.0235-0.0246-0.02630.0251-0.0257-0.02910.02250.02460.1615-0.26560.21440.2037-0.07230.150114.968225.1038.663
100.10580.0141-0.01790.0938-0.02030.00750.0001-0.0309-0.03040.03440.0276-0.1831-0.00130.11240.0878-0.0303-0.0137-0.00480.1917-0.06240.150612.990215.970413.9765
110.0480.0180.01460.0220.02660.0343-0.0061-0.00360.0129-0.00850.00980.0023-0.02430.01170.00930.1609-0.0366-0.09660.08870.00880.1025-5.792527.68179.3591
120.0003-0.00010.00120.0248-0.00550.0042-0.0350.0402-0.0141-0.04520.0349-0.0322-0.04660.0475-0.02340.215-0.19620.1470.2017-0.01910.01477.791621.6134.637
130.1093-0.04320.00170.0715-0.00630.0018-0.0226-0.0153-0.015-0.12450.02970.0876-0.0371-0.00110.07020.0793-0.0702-0.1690.0141-0.0714-0.0983-5.214215.29024.9924
140.0897-0.0358-0.01330.0418-0.02050.0325-0.0405-0.08230.0168-0.0053-0.02850.0699-0.0171-0.0538-0.04080.131-0.0846-0.06870.0973-0.03070.0658-8.047810.123511.1117
150.00810.00930.00220.01140.00260.00070.01870.014-0.00530.0011-0.00110.0080.00190.00380.00660.1142-0.08070.00780.4011-0.00530.3946-16.59384.3414.7469
160.04460.0016-0.00630.01410.02150.0362-0.00360.0173-0.041-0.0342-0.00710.03860.0425-0.0421-0.01690.1904-0.1133-0.06170.1721-0.09020.2367-9.46790.87333.1225
170.0501-0.0140.04010.16110.03740.06420.0785-0.01270.03090.1146-0.01630.05110.01470.00480.07650.2734-0.06970.08090.1442-0.04490.1029-3.921211.342529.2516
180.01320.023-0.02090.0533-0.04640.0404-0.0190.0062-0.0295-0.03440.01250.0280.072-0.0302-0.00950.3413-0.1520.12140.30450.05860.3016-8.9310.109322.9687
190.0142-0.0021-0.00090.0067-0.00030.00490.0043-0.0337-0.00670.01960.02110.00580.0176-0.05610.00010.6007-0.1632-0.02330.3811-0.05430.6201-10.848-10.16718.5714
200.02620.00190.0038-0.00020.0010.00440.01630.0179-0.0196-0.02570.0241-0.02860.00730.01520.10190.1054-0.00890.0213-0.039-0.08440.02212.0452-1.57425.9806
210.01190.0019-0.00130.0081-0.00010.0006-0.0032-0.01860.02590.05310.0244-0.0103-0.01-0.00080.07730.53340.0782-0.25960.1627-0.02060.243717.680841.961650.4719
220.01270.0143-0.02340.0187-0.0360.093-0.06310.0706-0.0881-0.0124-0.0143-0.08020.0179-0.0161-0.24580.0358-0.082-0.00820.1638-0.01590.146815.46134.355326.6055
230.00220.0011-0.00160.0029-0.00060.00340.0083-0.00410.0137-0.01560.0012-0.02780.00810.0092-00.19540.0515-0.00130.4902-0.11040.483726.674730.010427.0497
240.00730.01130.00360.02750.00290.0066-0.00020.02650.0184-0.00350.0104-0.0147-0.01280.0324-0.00120.0945-0.07190.00210.3344-0.21140.540528.380743.662933.9019
250.0977-0.02110.0720.0045-0.02290.1014-0.0158-0.0160.04350.07530.0326-0.1037-0.01810.01860.0763-0.0736-0.0269-0.21360.0176-0.05910.00915.943636.831236.401
260.049-0.01550.0220.0448-0.00070.0263-0.0004-0.00040.0058-0.00460.011-0.01660.0030.01130.02330.19840.0827-0.22170.1383-0.06260.297526.503733.532940.3984
270.0058-0.0216-0.00040.0648-0.00490.0035-0.0850.05740.0550.11-0.0174-0.0854-0.0047-0.0202-0.14340.0884-0.0295-0.05730.0958-0.02090.13187.662634.373833.3358
280.0002-0-0.00010.0028-0.00060.0009-0.00380.00910.00850.0097-0.00170.0092-0.0006-0.023300.436-0.11840.15890.4131-0.03070.4353-7.010623.737431.1458
290.0535-0.0147-0.04420.02280.00690.0375-0.05640.0394-0.04530.0632-0.02940.05140.0695-0.071-0.20840.5058-0.18810.3040.2042-0.06320.1441-0.556227.802542.2702
300.09510.12660.09580.24030.02790.2498-0.02440.0150.02360.1061-0.04610.0911-0.0018-0.0957-0.02590.2395-0.0016-0.01420.08550.00250.05288.860232.796840.7701
310.00150.001-0.00220.0058-0.00740.0102-0.04110.01330.0038-0.0252-0.02850.0216-0.0277-0.01220.00010.15010.0277-0.04330.3414-0.10620.4474-7.552440.789427.4395
320.01450.00910.00390.00480.00410.0019-0.0260.0209-0.02770.0723-0.02380.05770.0273-0.0358-0.0890.2074-0.20440.33710.2016-0.09870.309-2.627136.472341.5982
330.211-0.03770.07490.04350.07980.2758-0.00740.09630.04530.0047-0.15790.2625-0.0157-0.1329-0.30410.10490.01060.04170.1339-0.07420.2792-1.405549.411535.2444
340.03690.02050.02420.01790.01040.0175-0.10020.110.0181-0.1199-0.00980.1595-0.09350.0063-0.00340.2112-0.0170.04280.1443-0.00310.32435.391352.324931.1836
350.0015-0.00110.00030.0007-0.00050.0038-0.01870.02750.0061-0.0471-0.02030.01160.01860.002200.41450.0211-0.06720.26340.12480.27519.653860.558425.3094
360.01190.0024-0.01610.005-0.0070.0233-0.05360.0006-0.030.0586-0.03970.03080.0324-0.029-0.01080.1912-0.007-0.04290.0557-0.03180.24156.496861.777238.9691
370.10640.0003-0.00970.04950.01380.0057-0.01750.07250.0169-0.050.0187-0.0363-0.0261-0.0167-0.07290.1842-0.09560.12280.194-0.04730.194517.368542.033321.101
380.02230.01290.0220.01040.0170.0282-0.02410.0308-0.0595-0.07110.01-0.05760.0610.0069-0.00070.2811-0.14620.08250.1729-0.00540.24320.013754.645826.3031
390.02910.0120.00550.0256-0.00020.03340.0097-0.0160.00660.01170.0066-0.01170.0004-0.0020.01730.2136-0.1235-0.04250.0530.02950.225917.509967.399938.4613
400.0241-0.00480.00290.0013-00.0010.0055-0.00180.01450.05180.0196-0.00290.03440.00570.00630.2959-0.0127-0.01920.0808-0.01770.127513.176954.00845.3946
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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