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- PDB-3i07: Crystal structure of a putative organic hydroperoxide resistance ... -

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Basic information

Entry
Database: PDB / ID: 3i07
TitleCrystal structure of a putative organic hydroperoxide resistance protein from Vibrio cholerae O1 biovar eltor str. N16961
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / CSGID / Organic hydroperoxide resistance / NIAID / Structural Genomics / National Institute for Allergy and Infectious Disease (NIAID) / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


response to oxidative stress / metal ion binding
Similarity search - Function
Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta ...Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Organic hydroperoxide resistance protein, putative
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsNocek, B. / Maltseva, N. / Kwon, K. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: High resolution structural studies of the organic hydroperoxide resistance protein from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Nocek, B. / Maltseva, N. / Kwon, K. / Anderson, W. / Joachimiak, A.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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: Organic hydroperoxide resistance protein
B: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0645
Polymers30,6852
Non-polymers3793
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint-47 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.026, 76.154, 79.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Organic hydroperoxide resistance protein


Mass: 15342.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC_A1006 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KKU4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE IS UNKNOWN DENSITY FEATURES CLOSE TO THE CATALYTIC CYSTEIN RESIDUES, WHICH HAS BEEN MODELED ...THERE IS UNKNOWN DENSITY FEATURES CLOSE TO THE CATALYTIC CYSTEIN RESIDUES, WHICH HAS BEEN MODELED AS GLYCEROL RESIDUES (301,302).

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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: 1.88 Å3/Da / Density % sol: 34.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 Cesium chloride 0.1 M MES 30% Jeffamine M-600, pH 6.5, VAPOR DIFFUSION, SITTING 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 315r / Detector: CCD / Date: Dec 20, 2008 / 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: 1.5→20 Å / Num. all: 37820 / Num. obs: 35847 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 27
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.9 / Num. unique all: 995 / % possible all: 52.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 3EER
Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.785 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.9 / σ(I): 1.9 / ESU R: 0.083 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18454 1785 5 %RANDOM
Rwork0.16531 ---
obs0.16626 34011 95.11 %-
all-35796 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---0.95 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 24 275 2417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222248
X-RAY DIFFRACTIONr_bond_other_d0.0010.021426
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9663078
X-RAY DIFFRACTIONr_angle_other_deg0.91733543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8645320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.64225.63287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04615354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.466159
X-RAY DIFFRACTIONr_chiral_restr0.0870.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02407
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7281.51498
X-RAY DIFFRACTIONr_mcbond_other0.2271.5618
X-RAY DIFFRACTIONr_mcangle_it1.21922403
X-RAY DIFFRACTIONr_scbond_it2.0713750
X-RAY DIFFRACTIONr_scangle_it3.2214.5662
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.542 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 104 -
Rwork0.231 1696 -
obs--65.86 %
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)
14.2755-0.77691.634610.07482.41045.18240.16820.04080.51170.1998-0.1745-1.29810.30020.72840.00630.11150.02680.01790.15710.06230.25443.3741.397-23.772
217.8543-6.7529-2.4144.77990.43172.83430.3630.3182-0.2867-0.3243-0.30970.19680.31490.1378-0.05330.13760.0019-0.02540.0526-0.00860.0656-8.448-2.419-27.057
30.6582-1.0873-0.05441.9622-0.08461.15880.01660.0513-0.17490.014-0.0880.4364-0.0876-0.13270.07140.02910.00810.01950.1189-0.02770.2274-18.29117.741-25.582
46.53110.33963.45849.19422.519914.30830.20180.2051-0.6626-0.166-0.10550.77390.266-0.4992-0.09630.0211-0.0213-0.01840.1115-0.03350.2419-22.8197.599-26.384
51.2865-2.53270.038714.04666.67915.0858-0.1003-0.2776-0.1935-0.00770.06410.3459-0.0993-0.41730.03620.14840.00820.08440.18390.00520.1696-22.74115.377-19.913
67.0437-5.08444.71657.0094-1.31564.4688-0.6653-0.57730.30790.22870.4643-0.2327-0.5979-0.37230.2010.1680.10550.00130.1739-0.03330.0916-15.72628.598-13.149
77.7121-1.663-0.92944.758-1.7283.95720.1254-0.06820.33780.09150.17780.4472-0.3032-0.3368-0.30320.07750.04310.02390.09370.00170.1662-18.81622.424-14.196
80.81160.14720.49852.9729-1.47461.3917-0.0322-0.0256-0.00840.05760.02840.1239-0.0142-0.09050.00380.06740.01890.01360.0723-0.00530.0733-10.41311.901-12.893
91.0659-1.11830.10815.7203-2.48851.25520.02960.0274-0.1026-0.0156-0.0080.16630.00960.0013-0.02170.12050.00150.03630.05830.00890.0931-6.499-2.112-8.533
104.4978-1.2203-3.24948.45091.04486.6020.14120.0241-0.1668-0.1833-0.02970.2225-0.2854-0.108-0.11160.0921-0.0040.01940.04250.01170.0762-6.093-11.126-5.032
113.7692-0.31662.670813.3474-3.2393.68620.1499-0.3761-0.3270.67050.05220.59070.185-0.1542-0.20210.1270.00520.05110.06740.03050.0966-12.2120.067-1.274
120.98822.0593-1.76835.0504-4.46165.00310.0997-0.10240.10510.2834-0.05040.1249-0.17850.1038-0.04930.08680.00950.01720.0589-0.01090.0778-4.36420.274-11.231
134.74756.5566-1.686414.2239-6.29279.0419-0.13090.0702-0.036-0.2084-0.0055-0.3677-0.03460.36690.13640.0605-0.0025-0.00230.0347-0.01060.06651.44927.053-19.975
140.19210.8866-0.91865.68-4.25384.43990.00810.01170.01910.21920.02480.0026-0.0642-0.0703-0.03290.09710.0079-0.00570.09680.00050.092-3.23713.183-7.917
1510.9538-2.67460.92959.5652-5.10848.3526-0.18170.11070.113-0.01690.3850.0389-0.0169-0.4131-0.20330.3006-0.07060.01710.10340.01950.0112-3.226-0.7783.862
163.24130.5824-1.54889.6641-1.40916.337-0.0673-0.264-0.03390.5864-0.2312-0.5289-0.56890.360.29850.1864-0.0161-0.00450.07330.04740.11382.757-2.8520.095
172.1627-2.7281.67597.2312-0.55451.94110.0545-0.01020.13680.0403-0.1084-0.32540.0749-0.06450.05390.10170.0019-0.00740.06990.00670.07911.850.889-9.019
181.60531.04680.08442.43271.28512.26260.02470.0702-0.00270.1339-0.0345-0.09460.19010.00020.00990.09260.00190.00190.06130.0070.0786-1.8465.386-16.493
190.74180.1784-1.49641.4438-2.07479.44360.0383-0.0309-0.04140.1984-0.0577-0.1368-0.2640.30860.01940.0658-0.0169-0.01760.0737-0.00440.09723.3811.846-11.769
209.43436.3791-6.36210.2269-6.577914.92080.3077-0.629-0.41510.5126-0.6484-0.75420.05651.01070.34070.1796-0.0181-0.07830.12780.04270.06691.276.2811.363
216.6266-6.7244-2.8466.86152.75121.725-0.1043-0.12940.05120.1620.0557-0.0793-0.1840.30670.04860.1332-0.1106-0.02380.18860.02220.12616.40320.335-19.004
2215.9643.9362-2.36673.2276-1.30584.72280.041-0.08510.32620.1689-0.07050.0149-0.37060.20940.02950.1299-0.0030.0010.0448-0.00980.0679-3.46826.375-10.977
232.8655.0713-1.553519.8904-3.22982.87120.0345-0.0559-0.09450.3275-0.0907-0.14260.001-0.09450.05610.06560.00630.04280.08730.0010.0615-1212.203-5.937
244.35531.5559-0.985219.22883.31856.4549-0.0468-0.1622-0.21720.44080.02030.20350.5812-0.43750.02650.0933-0.02950.03980.14290.01670.1049-17.7156.127-7.393
253.63586.41261.030824.32612.88489.71370.0828-0.02630.4558-0.0639-0.44741.0833-0.1866-0.40630.36460.10230.13790.02660.3324-0.04560.2178-20.90814.63-8.23
262.3982-0.5791-0.046814.213613.500815.28270.088-0.2432-0.18940.27970.2372-0.23980.60990.1214-0.32520.1954-0.08520.03550.10160.04440.1324-18.309-1.201-15.653
273.25044.42940.507611.84134.91983.1594-0.10830.0063-0.08650.1632-0.02720.09130.2187-0.03530.13550.1682-0.09980.02510.10430.06140.1406-18.599-2.348-18.5
283.8318-1.40591.244113.8085-0.696310.09670.07140.005-0.22180.0008-0.060.33030.2968-0.2506-0.01140.0587-0.05020.03070.0885-0.00320.0929-14.295.774-19.036
290.79561.22480.72522.43530.36281.69450.0408-0.07220.04370.0294-0.08940.0580.0894-0.10150.04860.0596-0.02020.02070.0874-0.00070.0938-11.55313.023-22.633
301.7291.661-0.36265.7876-0.97170.84890.0206-0.07920.12950.0886-0.02490.0148-0.06050.00320.00430.040.0001-0.00630.0718-0.01410.0935-10.33724.542-27.588
3114.817212.82612.483914.25552.696910.46370.2719-0.09430.47680.2369-0.07260.7056-0.3572-0.2659-0.19930.11520.03720.00790.0229-0.01520.1783-10.13433.941-31.771
323.8059-5.52120.598926.8198-4.88194.40950.07050.07920.0151-0.21470.06880.8866-0.2504-0.309-0.13930.0482-0.0006-0.00740.1022-0.00990.083-16.8522.149-32.79
331.4648-2.72311.88335.2409-3.12443.27510.15680.0434-0.0615-0.2458-0.07220.12210.30460.0136-0.08460.0833-0.0005-0.01550.06370.00560.0934-5.8541.545-24.999
344.9326-6.04163.769114.2329-5.22437.3854-0.04180.05430.11590.1331-0.015-0.32350.29390.29640.05680.08550.0007-0.00840.043-0.00530.062-0.602-1.428-20.207
352.9661-3.70592.34444.6901-3.3314.7230.06010.10040.0075-0.0512-0.0949-0.0297-0.1374-0.14580.03480.07740.0113-0.00070.10010.00780.0763-10.59316.827-34.37
3611.0629-3.03623.70116.187-0.866110.1976-0.0480.08970.0704-0.27620.08550.1868-0.2765-0.5214-0.03750.120.0030.00730.09180.02190.0786-5.94225.746-42.967
371.11180.9601-0.64111.11540.04561.65520.02410.0246-0.084-0.09550.0015-0.1241-0.2126-0.0714-0.02560.11720.01480.03070.07820.01460.095-2.21223.532-33.504
381.26970.4421-0.344.14841.052.5680.0153-0.00980.0217-0.0139-0.0659-0.0606-0.0983-0.01370.05050.0518-0.005-0.00490.05950.00620.0738-2.91218.346-22.198
394.2926-1.2975.37740.968-2.15357.22670.25620.1908-0.1363-0.2152-0.1192-0.02420.45150.2945-0.13690.08390.02560.00640.0868-0.00060.12030.5211.109-27.782
409.3804-1.00415.13931.5534-2.73556.1202-0.17190.23750.13170.05350.0151-0.0664-0.15920.08060.15680.1412-0.0175-0.00320.08010.00030.0637-6.71316.77-39.207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 11
3X-RAY DIFFRACTION3A12 - 25
4X-RAY DIFFRACTION4A26 - 30
5X-RAY DIFFRACTION5A31 - 35
6X-RAY DIFFRACTION6A36 - 43
7X-RAY DIFFRACTION7A44 - 50
8X-RAY DIFFRACTION8A51 - 61
9X-RAY DIFFRACTION9A62 - 70
10X-RAY DIFFRACTION10A71 - 77
11X-RAY DIFFRACTION11A78 - 82
12X-RAY DIFFRACTION12A83 - 91
13X-RAY DIFFRACTION13A92 - 97
14X-RAY DIFFRACTION14A98 - 104
15X-RAY DIFFRACTION15A105 - 110
16X-RAY DIFFRACTION16A111 - 116
17X-RAY DIFFRACTION17A117 - 122
18X-RAY DIFFRACTION18A123 - 130
19X-RAY DIFFRACTION19A131 - 138
20X-RAY DIFFRACTION20A139 - 145
21X-RAY DIFFRACTION21B-2 - 4
22X-RAY DIFFRACTION22B5 - 10
23X-RAY DIFFRACTION23B11 - 18
24X-RAY DIFFRACTION24B19 - 27
25X-RAY DIFFRACTION25B28 - 33
26X-RAY DIFFRACTION26B34 - 39
27X-RAY DIFFRACTION27B40 - 48
28X-RAY DIFFRACTION28B49 - 53
29X-RAY DIFFRACTION29B54 - 58
30X-RAY DIFFRACTION30B59 - 70
31X-RAY DIFFRACTION31B71 - 77
32X-RAY DIFFRACTION32B78 - 83
33X-RAY DIFFRACTION33B84 - 92
34X-RAY DIFFRACTION34B93 - 98
35X-RAY DIFFRACTION35B99 - 108
36X-RAY DIFFRACTION36B109 - 113
37X-RAY DIFFRACTION37B114 - 122
38X-RAY DIFFRACTION38B123 - 130
39X-RAY DIFFRACTION39B131 - 137
40X-RAY DIFFRACTION40B138 - 145

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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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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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