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- PDB-3iuo: The Crystal Structure of the C-terminal domain of the ATP-depende... -

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Basic information

Entry
Database: PDB / ID: 3iuo
TitleThe Crystal Structure of the C-terminal domain of the ATP-dependent DNA helicase RecQ from Porphyromonas gingivalis to 1.6A
ComponentsATP-dependent DNA helicase RecQ
KeywordsHYDROLASE / ATP-dependent / helicase / RecQ / C-terminal / porphyromonas / gingivalis / PSI / MCSG / Structural Genomics / Midwest Center for Structural Genomics / Protein Structure Initiative / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


3'-5' DNA helicase activity / SOS response / DNA recombination / DNA replication / DNA helicase / DNA repair / DNA binding / ATP binding
Similarity search - Function
ATP-dependent DNA helicase RecQ / DNA helicase, ATP-dependent, RecQ type, bacterial / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain ...ATP-dependent DNA helicase RecQ / DNA helicase, ATP-dependent, RecQ type, bacterial / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC-like superfamily / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsStein, A.J. / Sather, A. / Duggan, E. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The Crystal Structure of the C-terminal domain of the ATP-dependent DNA helicase RecQ from Porphyromonas gingivalis to 1.6A
Authors: Stein, A.J. / Sather, A. / Duggan, E. / Moy, S. / Joachimiak, A.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent DNA helicase RecQ
B: ATP-dependent DNA helicase RecQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1194
Polymers29,0612
Non-polymers582
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-23 kcal/mol
Surface area12370 Å2
MethodPISA
2
A: ATP-dependent DNA helicase RecQ
B: ATP-dependent DNA helicase RecQ
hetero molecules

A: ATP-dependent DNA helicase RecQ
B: ATP-dependent DNA helicase RecQ
hetero molecules

A: ATP-dependent DNA helicase RecQ
B: ATP-dependent DNA helicase RecQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,35812
Polymers87,1836
Non-polymers1756
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8090 Å2
ΔGint-106 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.326, 98.326, 72.526
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Detailsauthors state that biological unit is same as asymmetric unit.

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Components

#1: Protein ATP-dependent DNA helicase RecQ


Mass: 14530.452 Da / Num. of mol.: 2 / Fragment: residues 604-725
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG0684, PG_0416, recQ-1 / Plasmid: pMCSG8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7MX11
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 35% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Jun 30, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 34286 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Χ2: 3.351 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.664.10.49335040.9781100
1.66-1.724.10.33434480.9711100
1.72-1.84.10.22834451.0321100
1.8-1.94.10.17134561.2791100
1.9-2.024.10.11334861.7391100
2.02-2.174.10.08734212.514199.9
2.17-2.394.10.07834923.451199.8
2.39-2.744.10.07734365.022199.4
2.74-3.4540.06934036.582198.3
3.45-503.70.073319511.664192.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
Cootmodel building
RefinementResolution: 1.6→24.07 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.198 / SU B: 3.313 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1726 5 %RANDOM
Rwork0.188 ---
obs0.19 34256 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.889 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 2 182 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221843
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9762492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5385231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70825.31994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60515360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5331511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021365
X-RAY DIFFRACTIONr_mcbond_it0.7271.51117
X-RAY DIFFRACTIONr_mcangle_it1.25621822
X-RAY DIFFRACTIONr_scbond_it2.493726
X-RAY DIFFRACTIONr_scangle_it3.844.5664
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.598-1.6390.3121330.2662387255498.669
1.639-1.6840.266980.2492393249599.84
1.684-1.7320.2531320.2192313244899.877
1.732-1.7850.2431100.2122214232699.914
1.785-1.8430.2381240.1892129225899.779
1.843-1.9080.1971000.1652125222699.955
1.908-1.9790.1741080.1620012109100
1.979-2.060.1961070.1651962207099.952
2.06-2.150.2051020.1611863196699.949
2.15-2.2540.21800.1651798188099.894
2.254-2.3750.228990.1791670177599.662
2.375-2.5180.202910.191588168699.585
2.518-2.690.219700.2041526160999.192
2.69-2.9020.236830.2061379148098.784
2.902-3.1740.236800.1921263136398.533
3.174-3.5410.213670.1851138123597.571
3.541-4.0750.167560.171013109997.27
4.075-4.9550.214480.16783091895.643
4.955-6.8630.291300.22767773795.929
6.863-24.0710.47580.23526142463.443
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)
111.29352.8128-0.03783.14930.8786.3795-0.0050.61180.3085-0.30780.10510.2471-0.0926-0.4284-0.10010.16230.0190.00350.15780.01140.134411.9823-13.168139.1886
28.24975.7305-3.210313.7654-3.23019.17820.04110.28490.1273-0.34560.13250.51630.0838-0.2919-0.17360.12230.01310.03110.0981-0.02660.103817.748-8.319639.299
34.2677-0.69271.82857.96240.33274.1254-0.05450.1682-0.0796-0.28170.0493-0.36530.05690.1830.00520.13180.03140.070.0869-0.01960.074322.0637-1.25337.0753
48.8772-2.9931-0.288510.57360.15148.95640.04960.53080.237-0.80550.0736-0.82710.08880.1808-0.12320.2566-0.00470.12870.14680.01290.178923.77265.945432.7003
58.47221.2038-3.88447.6722-0.17956.2020.15250.4610.4372-0.5551-0.00630.218-0.0081-0.2875-0.14610.24230.00990.00110.15520.02540.091215.2837.412832.504
610.74111.5307-3.88167.99211.707610.8749-0.2240.8181-0.7468-0.4712-0.00920.41710.4363-0.26910.23320.2907-0.0332-0.02310.2106-0.07020.175511.31030.313733.2704
74.5248-3.31481.490410.84362.007310.89630.12020.3032-0.0847-0.5374-0.10480.62470.1628-0.4926-0.01550.1282-0.0322-0.04070.11210.00620.11369.25564.878940.0482
812.1473-3.40681.23795.14860.30047.17380.0620.0483-0.39390.05870.07880.04570.38830.0824-0.14070.09610.01210.01010.0302-0.01620.067117.19052.510945.3127
94.8182-2.30655.99427.9773-2.33337.50870.19820.84410.0609-0.4185-0.2308-0.38570.28971.10230.03260.21970.11520.03670.32610.02710.171524.5712.755647.3824
104.61590.1348-1.209711.4166-3.2699.05230.1286-0.21290.1787-0.0935-0.1198-0.5366-0.02460.2769-0.00880.1342-0.00250.08510.10450.01530.191322.874911.988238.5791
116.9998-4.8715-3.399312.19745.32625.63510.21010.31740.237-0.3799-0.3332-0.1643-0.1421-0.40160.12310.21640.00430.06160.13350.07270.115216.895517.098536.2652
127.7525-1.2562-0.32689.74250.903913.86540.01490.30340.4001-0.4309-0.0957-0.2306-0.20670.13430.08080.18250.01020.01420.13290.05870.174114.030724.568841.5411
133.70180.3213-0.02854.7666-2.459411.1513-0.04460.06860.422-0.0281-0.0568-0.3578-0.69080.30040.10140.0932-0.0245-0.00740.03550.01360.149817.48222.05649.8634
142.7692-0.7624-0.13980.9912-2.55058.62950.06290.04410.21520.092-0.096-0.0926-0.3150.29920.03310.1025-0.0095-0.04890.0797-0.01080.15518.847717.276657.5801
158.2419-0.6722-2.83929.47592.10549.4172-0.0947-0.2851-0.25310.10350.03670.17280.2137-0.37520.0580.1012-0.0252-0.01440.08290.0090.060711.620811.315356.9532
1612.1111-0.0946-3.79816.3618-14.101516.6586-0.092-0.03160.09690.08170.22860.0859-0.1703-0.4482-0.13660.10540.03720.00150.15160.02240.09998.063517.874655.5498
177.698-3.7468-0.96211.94481.98247.2676-0.1533-0.17510.05580.30430.17580.3752-0.086-0.4444-0.02250.06340.02330.00210.07620.04880.0676.597918.317247.9014
184.7952-1.3267-0.44564.9182-0.95082.7520.03830.1230.1036-0.2545-0.0586-0.182-0.0870.0640.02030.040.00050.00490.0060.00640.03615.000913.209746.424
1912.2212.47065.820713.79060.21710.22270.0688-0.8332-0.05340.4059-0.0799-0.9591-0.1840.79690.01110.1459-0.00790.0340.25730.00050.280524.201612.154949.8017
2016.71454.9777-2.3382.2986-3.60910.7488-0.2513-0.553-0.1908-0.1882-0.0125-0.1160.4135-0.21310.26380.2430.0077-0.02370.4012-0.05450.288-1.00417.91175.2205
2111.1941-5.34691.64159.07783.8410.73010.0836-0.33030.03790.02380.01630.4109-0.0016-0.8201-0.09990.1408-0.02-0.00760.3406-0.0660.22736.128518.503576.0187
227.8044-3.12432.33846.4734-2.84019.0744-0.1476-0.58240.54940.4040.06730.3212-0.3589-0.13690.08030.1522-0.0204-0.01870.2126-0.07950.115313.222217.871679.9589
2318.4189-0.7083-1.33247.862-0.536510.9063-0.2505-0.87820.62750.70170.1088-0.2502-0.07680.02710.14170.2027-0.0397-0.05990.239-0.04030.074219.182514.602583.0669
247.0276-1.24092.68291.58351.42263.71320.1019-0.2295-0.40660.4811-0.0380.07660.6714-0.1857-0.0640.3088-0.064-0.01040.29030.03480.186515.15256.976982.7012
255.6724-0.5007-1.5813.57853.372412.6964-0.0161-0.4916-0.03130.3855-0.34840.71210.2231-0.6020.36460.1846-0.11720.08180.36410.0020.20766.84287.342681.4954
265.24342.8316-6.536610.0519-0.027612.63790.0063-0.4704-0.29690.4843-0.22370.46410.5196-0.20050.21740.1195-0.1250.00920.30340.07160.23369.89864.896374.4441
275.3036-0.0182-0.24466.03360.48814.93250.037-0.15030.0870.0978-0.06640.2327-0.0514-0.21630.02940.0412-0.0161-0.01030.1017-0.03480.071613.995714.028369.1219
281.90513.1177-2.55328.9835-6.56054.8851-0.0071-0.1769-0.0690.0215-0.1439-0.2232-0.00090.15360.15110.2106-0.0419-0.05670.179-0.00260.141423.753712.468774.4125
299.60822.17061.067418.54583.61327.33530.0421-0.2456-0.76150.4065-0.1185-0.11690.49020.33030.07650.26910.0099-0.05270.25120.06280.130623.65284.503679.6636
300.9803-1.5783-3.72148.68554.391514.7047-0.1356-0.1253-0.11970.7163-0.07770.29690.35590.33130.21330.41820.0214-0.07090.3690.19780.3726.1976-3.793974.5651
318.4332-1.3292-0.93211.41722.92948.4554-0.1879-0.3859-0.1330.48310.1548-0.84580.4690.62910.03320.13340.047-0.07950.14050.04590.203428.3244-0.04868.0091
3212.2065-1.3511.62596.3068-0.94359.8590.04910.1688-0.02170.0247-0.0846-0.61670.08140.77010.03550.07180.0265-0.03810.09490.01750.146127.49392.446761.182
336.0738-2.3685-0.71742.20611.09488.0890.0815-0.1059-0.2750.0379-0.24060.05130.3087-0.40190.15920.09670.0141-0.0260.0933-0.01520.098418.49913.831557.7932
3424.6233-2.2515.233418.4862-8.186526.98390.3820.03-0.49240.0925-0.38780.19111.2893-0.16470.00580.2651-0.0559-0.00560.078-0.0340.224317.9917-3.281358.1244
351.571-2.3543-0.288414.203-12.627116.0345-0.20530.0274-0.2479-0.6617-0.10070.14841.19890.08980.3060.4038-0.03130.04590.1696-0.00950.403520.6402-8.191464.8084
366.02862.6155-1.62789.4917-0.97118.01880.0787-0.102-0.29340.2324-0.05510.55140.4278-0.2966-0.02360.1603-0.0291-0.01090.09770.01960.150216.5936-2.238469.7798
371.74030.8763-1.79935.29061.4553.4997-0.1102-0.19770.0060.2754-0.02120.07030.2833-0.02170.13140.0724-0.0082-0.02830.18-0.03190.052418.37064.910268.8169
381.76671.4547-0.576111.3217-1.38233.0492-0.0105-0.045-0.0851-0.0905-0.0087-0.30090.11340.25440.01920.0874-0.0142-0.0350.1338-0.02540.130624.506812.101766.5472
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A614 - 619
2X-RAY DIFFRACTION2A620 - 624
3X-RAY DIFFRACTION3A625 - 630
4X-RAY DIFFRACTION4A631 - 635
5X-RAY DIFFRACTION5A636 - 641
6X-RAY DIFFRACTION6A642 - 647
7X-RAY DIFFRACTION7A648 - 653
8X-RAY DIFFRACTION8A654 - 660
9X-RAY DIFFRACTION9A661 - 665
10X-RAY DIFFRACTION10A666 - 670
11X-RAY DIFFRACTION11A671 - 675
12X-RAY DIFFRACTION12A676 - 680
13X-RAY DIFFRACTION13A681 - 687
14X-RAY DIFFRACTION14A688 - 693
15X-RAY DIFFRACTION15A694 - 698
16X-RAY DIFFRACTION16A699 - 704
17X-RAY DIFFRACTION17A705 - 710
18X-RAY DIFFRACTION18A711 - 718
19X-RAY DIFFRACTION19A719 - 723
20X-RAY DIFFRACTION20B615 - 620
21X-RAY DIFFRACTION21B621 - 625
22X-RAY DIFFRACTION22B626 - 630
23X-RAY DIFFRACTION23B631 - 635
24X-RAY DIFFRACTION24B636 - 641
25X-RAY DIFFRACTION25B642 - 648
26X-RAY DIFFRACTION26B649 - 654
27X-RAY DIFFRACTION27B655 - 664
28X-RAY DIFFRACTION28B665 - 669
29X-RAY DIFFRACTION29B670 - 674
30X-RAY DIFFRACTION30B675 - 680
31X-RAY DIFFRACTION31B681 - 685
32X-RAY DIFFRACTION32B686 - 690
33X-RAY DIFFRACTION33B691 - 697
34X-RAY DIFFRACTION34B698 - 702
35X-RAY DIFFRACTION35B703 - 707
36X-RAY DIFFRACTION36B708 - 712
37X-RAY DIFFRACTION37B713 - 717
38X-RAY DIFFRACTION38B718 - 725

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Jul 12, 2017. Major update of PDB

Major update of PDB

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

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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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