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- PDB-3efp: Crystal structure of the Escherichia coli twin arginine leader pe... -

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Basic information

Entry
Database: PDB / ID: 3efp
TitleCrystal structure of the Escherichia coli twin arginine leader peptide binding protein DmsD in a monomeric form
ComponentsTwin-arginine leader-binding protein dmsD
KeywordsCHAPERONE / twin-arginine translocation (Tat) / protein targeting / protein translocation / leader peptide / signal peptide / redox enzyme maturation protein (REMP)
Function / homology
Function and homology information


signal sequence binding / chaperone-mediated protein folding / plasma membrane / cytoplasm
Similarity search - Function
Tat proofreading chaperone DmsD-type / Tat proofreading chaperone DmsD / TorD-like / TorD-like / DMSO/Nitrate reductase chaperone / TorD-like superfamily / Nitrate reductase delta subunit / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tat proofreading chaperone DmsD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.01 Å
AuthorsStevens, C.M. / Paetzel, M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural analysis of a monomeric form of the twin-arginine leader peptide binding chaperone Escherichia coli DmsD.
Authors: Stevens, C.M. / Winstone, T.M. / Turner, R.J. / Paetzel, M.
History
DepositionSep 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Twin-arginine leader-binding protein dmsD
B: Twin-arginine leader-binding protein dmsD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,97919
Polymers47,7022
Non-polymers1,27717
Water7,404411
1
A: Twin-arginine leader-binding protein dmsD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,57010
Polymers23,8511
Non-polymers7199
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Twin-arginine leader-binding protein dmsD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4099
Polymers23,8511
Non-polymers5588
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.020, 128.020, 78.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Twin-arginine leader-binding protein dmsD


Mass: 23851.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dmsD, ynfI, b1591, JW5262 / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P69853

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Non-polymers , 5 types, 428 molecules

#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.25M ammonium sulfate, 12% glycerol, 0.1M Bis-Tris pH 6.5, 72 hours, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 16, 2007 / Details: Rigaku VariMAX HF
RadiationMonochromator: Nickel Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→30.75 Å / Num. all: 49796 / Num. obs: 48639 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.72 % / Biso Wilson estimate: 92.8 Å2 / Rmerge(I) obs: 0.089 / Χ2: 0.96 / Scaling rejects: 2102
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.01-2.085.580.3624.52652247031.1695.6
2.08-2.165.720.334.82744647591.0796.6
2.16-2.265.710.2885.32751947801.0496.7
2.26-2.385.720.2456.12770347951.0397
2.38-2.535.730.2086.8277814813197.6
2.53-2.735.740.16982814148600.9798
2.73-35.750.12410.12833348860.9398.5
3-3.435.780.08314.22866449250.8898.6
3.43-4.335.780.04722.82887949750.7999.3
4.33-30.755.650.03630.12916951430.7899.4

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
d*TREKdata reduction
PHASERphasing
RefinementStarting model: 1s9u
Resolution: 2.01→30.75 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.515 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2463 5.1 %RANDOM
Rwork0.178 ---
all0.236 49796 --
obs0.18 48639 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.39 Å2 / Biso mean: 22.692 Å2 / Biso min: 9.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.22 Å20 Å2
2--0.43 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.01→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3345 0 75 411 3831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223549
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.9454844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6445416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86323.626171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73615532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.41522
X-RAY DIFFRACTIONr_chiral_restr0.0730.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022754
X-RAY DIFFRACTIONr_nbd_refined0.2080.31676
X-RAY DIFFRACTIONr_nbtor_refined0.3160.52444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5510
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.359
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.535
X-RAY DIFFRACTIONr_mcbond_it0.3121.52103
X-RAY DIFFRACTIONr_mcangle_it0.55423379
X-RAY DIFFRACTIONr_scbond_it1.0231564
X-RAY DIFFRACTIONr_scangle_it1.5834.51465
LS refinement shellResolution: 2.009→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 164 -
Rwork0.27 3339 -
all-3503 -
obs--95.76 %
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)
17.197-3.08612.230211.2887-2.11597.1958-0.2079-0.98870.00750.78350.43430.4245-0.2762-0.3482-0.22640.0205-0.02460.01110.1155-0.0235-0.0052-50.126149.813738.9502
22.46160.9819-2.79261.03581.000710.1107-0.1247-0.16310.1293-0.07950.2083-0.1965-0.27520.9779-0.0836-0.0616-0.027-0.01650.12910.01110.0432-40.579442.973223.4825
35.22373.0444-5.40752.0523-1.961210.69430.0553-0.376-0.08440.24160.1181-0.20960.48370.9724-0.17330.0040.071-0.06940.2757-0.01940.0117-36.299736.04429.534
43.7996-1.6702-2.17877.65490.894611.1830.32-0.1887-0.61450.3865-0.17020.17830.65910.3947-0.1499-0.02980.027-0.08230.05350.05160.0526-46.147831.881335.1367
51.8351.88574.380210.03536.361212.834-0.06710.956-0.65420.23840.9738-0.76851.76232.2033-0.90670.24460.2736-0.08810.2961-0.10420.1631-38.7225.875424.5921
67.4172-1.53823.66192.1948-2.41356.33720.00780.0925-0.1804-0.0365-0.0593-0.1250.42340.70250.0515-0.02480.03630.01450.0671-0.0360.0107-41.266334.165811.105
72.3516-0.1011-0.17192.0271-1.1241.3868-0.06380.14060.0102-0.06220.0695-0.01010.09760.056-0.0058-0.0579-0.00620.0072-0.02780.0098-0.0476-54.770244.177512.5488
822.02556.1958-9.60484.8255-1.19166.7421-0.14341.3667-0.1309-0.46340.13950.07110.3168-0.27220.0039-0.0424-0.0101-0.00830.00050.0308-0.0307-60.01648.26436.7519
91.60210.2311-0.49870.4857-0.89281.6448-0.07310.0580.27240.1567-0.02640.0441-0.45930.04630.0995-0.0002-0.01330.0044-0.02620.01830.0113-54.843357.563215.5296
1012.2422-1.9196-1.039224.81310.389438.5178-0.10420.42161.82380.929-0.1862-0.113-1.313-0.8710.29050.1464-0.0603-0.03390.03920.01070.1952-51.867364.612522.6129
1118.2137-6.5129-11.62723.823213.148461.51410.51340.45631.202-0.9758-1.40050.3031-0.31881.49140.88710.1796-0.15760.04280.23890.10050.4563-41.998956.829318.2568
1221.0836-3.0272-17.760.82076.015346.06560.4333-0.52850.60770.33260.1404-0.6556-1.2491.3869-0.5736-0.0176-0.07790.0088-0.01560.01130.1263-44.695553.649810.6614
131.2838-0.13361.4190.0139-0.14771.5684-0.084-0.13460.0453-0.1356-0.0679-0.0193-0.3430.33470.152-0.0733-0.04320.00110.0218-0.01320.0239-46.966750.940524.0499
1419.87110.349-1.86354.00223.42115.6111-0.3418-0.44490.33530.11660.1833-0.2521-0.30570.15090.15860.0386-0.0278-0.023-0.0046-0.02470.024-48.166258.084534.0076
1511.5212-6.6366-0.75611.21218.770710.7495-0.13690.01240.76850.0571-0.1327-0.0535-0.35870.20880.2695-0.0438-0.03330.0015-0.0502-0.00640.0273-54.607555.757629.452
162.1934-1.1855-0.16252.37560.81452.15490.0610.0934-0.1269-0.0104-0.03110.06650.10410.0822-0.03-0.0776-0.007-0.0034-0.02790.0087-0.0446-53.631639.42120.4491
1718.1967-8.9245-5.00328.6004-0.174615.58370.25520.2138-0.9688-0.3835-0.25050.4640.75550.143-0.00470.01160.0311-0.0742-0.0142-0.0069-0.0078-45.886832.436322.1261
1812.1309-0.8891-2.20840.19721.335710.83760.4770.1417-0.899-0.0849-0.17740.4280.71890.0293-0.2995-0.01830.0098-0.06980.02650.01880.0413-51.69734.975827.8969
194.0352-3.1395-1.55332.45331.21630.6036-0.151-0.50390.21180.16990.17090.0581-0.01690.0489-0.0199-0.051-0.03170.00060.03040.01410.0115-55.163142.694332.3985
201.79671.09093.21182.26832.451710.7053-0.0532-0.16190.0029-0.09350.0124-0.0425-0.22870.18690.0407-0.1106-0.01330.03790.00870.0132-0.0212-62.761547.526223.5641
218.764-2.05572.94718.048617.185826.9463-0.97340.6958-1.61460.76771.6504-0.86080.2835-1.1195-0.67710.21230.11050.05870.314-0.08220.0507-3.874683.68535.5261
222.49560.3731-3.62817.8028-6.611815.05650.3241-0.51880.17470.2466-0.0702-0.2651-0.02940.3021-0.2539-0.0717-0.0110.03-0.0516-0.0105-0.0032-11.718172.312832.5341
233.1683.0024-0.35746.15790.16351.8171-0.05190.0910.0198-0.42380.02580.07240.1641-0.25030.0261-0.0498-0.0231-0.0191-0.00070.003-0.058-15.506859.138329.7596
246.88420.10092.02883.06831.68634.58230.10240.3879-0.3452-0.37830.0363-0.22620.3163-0.0139-0.13870.1065-0.04910.0168-0.0232-0.00030.036-13.263347.936326.3743
254.95562.1210.30954.9178-2.0811.24110.05310.0768-0.2276-0.19970.0098-0.25470.40550.0055-0.0629-0.0253-0.0036-0.0208-0.0441-0.0106-0.0111-4.511554.363336.296
269.6241.1698-5.56023.5586-5.40819.7674-0.2624-0.2227-1.3763-0.384-0.3956-0.17851.43880.09180.6580.3172-0.0178-0.0227-0.01150.01910.2195-9.371240.615435.424
276.82710.77060.38820.77233.5417.85690.0807-0.5021-0.79510.4827-0.0509-0.55761.4713-0.3896-0.02970.3609-0.1925-0.04550.01740.03390.2381-20.269936.845532.4087
2824.38422.52993.97561.3076-1.47574.05940.41680.1775-0.4781-0.47320.11180.40020.9238-0.4937-0.52860.1737-0.1942-0.03830.25670.00560.1181-29.7843.197234.1814
293.0274-1.64081.42642.32850.42213.94580.2259-0.317-0.14510.0703-0.28510.54310.1897-0.43110.0592-0.0386-0.15640.03990.1980.01970.0766-33.261655.326242.3072
304.44864.141-1.885410.6789-2.97214.11160.5286-0.82070.11440.7381-0.50520.68050.4614-0.5212-0.0234-0.0456-0.10590.03440.2892-0.04740.1054-39.067958.989139.985
3111.62588.9414-5.205815.8594-7.74435.45770.04950.36940.5002-0.09370.25461.1769-0.077-0.9772-0.3041-0.0498-0.02010.01430.1887-0.04890.0395-34.096268.727834.4916
3214.7069-2.14713.051942.5704-5.330925.42530.02840.4681.4019-0.6931-0.03151.1307-1.0776-1.53270.00310.00190.07170.0320.19460.01560.1709-31.492873.790328.6741
3317.706229.93220.90552.92983.987612.6117-0.7174-0.47380.5694-1.48710.19752.3814-0.132-2.02870.51990.0952-0.0586-0.12610.3976-0.04310.1192-30.133862.523323.4495
343.07662.5799-2.65633.4197-1.80432.436-0.06710.25540.117-0.0870.09150.19150.1236-0.503-0.0244-0.05-0.0291-0.00420.11020.01020.001-26.14862.382128.5109
3510.13672.4996-9.59697.1911-2.03719.10230.01380.22740.021-0.27680.06530.3105-0.3241-0.7764-0.0791-0.02160.007-0.01140.04050.00310.0542-20.179574.452430.4135
361.6076-0.5078-0.69415.46410.5591.17080.1239-0.2238-0.03360.3724-0.22520.10310.108-0.24180.1013-0.06-0.0931-0.00460.07950.0052-0.0193-23.159360.043241.7444
379.6866-15.437-2.382832.968311.47247.6263-1.4668-0.794-1.41010.10240.47241.72281.73740.06210.99440.1328-0.1264-0.01630.02780.04540.105-19.891341.746840.7042
386.63385.80671.939524.64897.24234.50680.1452-0.7653-0.52830.9934-0.05530.04310.71920.0992-0.08990.0356-0.0777-0.01370.06380.05790.0094-15.653347.491437.8809
392.98370.22940.292810.47430.22152.02910.0331-0.12190.18920.58190.1334-0.024-0.0299-0.0317-0.1665-0.0745-0.05740.0080.00740.0069-0.0307-13.887464.056540.7099
4011.90418.9521-8.519512.1877-9.86048.28350.6782-0.83470.34230.5051-0.5210.514-0.1567-0.1795-0.15730.0095-0.11740.03110.2082-0.0559-0.0083-28.966363.546847.8582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION2A12 - 26
3X-RAY DIFFRACTION3A27 - 44
4X-RAY DIFFRACTION4A45 - 59
5X-RAY DIFFRACTION5A60 - 64
6X-RAY DIFFRACTION6A65 - 82
7X-RAY DIFFRACTION7A83 - 93
8X-RAY DIFFRACTION8A94 - 98
9X-RAY DIFFRACTION9A99 - 110
10X-RAY DIFFRACTION10A111 - 115
11X-RAY DIFFRACTION11A116 - 120
12X-RAY DIFFRACTION12A121 - 125
13X-RAY DIFFRACTION13A126 - 139
14X-RAY DIFFRACTION14A140 - 145
15X-RAY DIFFRACTION15A146 - 150
16X-RAY DIFFRACTION16A151 - 174
17X-RAY DIFFRACTION17A175 - 179
18X-RAY DIFFRACTION18A180 - 184
19X-RAY DIFFRACTION19A185 - 191
20X-RAY DIFFRACTION20A192 - 204
21X-RAY DIFFRACTION21B-3 - 1
22X-RAY DIFFRACTION22B2 - 6
23X-RAY DIFFRACTION23B7 - 22
24X-RAY DIFFRACTION24B23 - 43
25X-RAY DIFFRACTION25B44 - 57
26X-RAY DIFFRACTION26B58 - 64
27X-RAY DIFFRACTION27B65 - 71
28X-RAY DIFFRACTION28B72 - 80
29X-RAY DIFFRACTION29B81 - 94
30X-RAY DIFFRACTION30B95 - 101
31X-RAY DIFFRACTION31B102 - 109
32X-RAY DIFFRACTION32B110 - 115
33X-RAY DIFFRACTION33B116 - 120
34X-RAY DIFFRACTION34B121 - 142
35X-RAY DIFFRACTION35B143 - 147
36X-RAY DIFFRACTION36B148 - 168
37X-RAY DIFFRACTION37B169 - 173
38X-RAY DIFFRACTION38B174 - 180
39X-RAY DIFFRACTION39B181 - 195
40X-RAY DIFFRACTION40B196 - 204

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