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- PDB-3oam: Crystal structure of cytidylyltransferase from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 3oam
TitleCrystal structure of cytidylyltransferase from Vibrio cholerae
Components3-deoxy-manno-octulosonate cytidylyltransferase
KeywordsTRANSFERASE / Center for Structural Genomics of Infectious Diseases / CSGID / Cytidylyltransferase
Function / homology
Function and homology information


3-deoxy-manno-octulosonate cytidylyltransferase / 3-deoxy-manno-octulosonate cytidylyltransferase activity / CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / lipopolysaccharide core region biosynthetic process / cytosol
Similarity search - Function
3-deoxy-D-manno-octulosonate cytidylyltransferase / Acylneuraminate cytidylyltransferase / Cytidylyltransferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
3-deoxy-manno-octulosonate cytidylyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHattne, J. / Borek, D. / Grimshaw, S. / Nakka, C. / Rostankowski, R. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of cytidylyltransferase from Vibrio cholerae
Authors: Hattne, J. / Borek, D. / Grimshaw, S. / Nakka, C. / Rostankowski, R. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 3-deoxy-manno-octulosonate cytidylyltransferase
B: 3-deoxy-manno-octulosonate cytidylyltransferase
C: 3-deoxy-manno-octulosonate cytidylyltransferase
D: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,0225
Polymers110,9994
Non-polymers231
Water12,430690
1
A: 3-deoxy-manno-octulosonate cytidylyltransferase
B: 3-deoxy-manno-octulosonate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5223
Polymers55,4992
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-22 kcal/mol
Surface area21920 Å2
MethodPISA
2
C: 3-deoxy-manno-octulosonate cytidylyltransferase
D: 3-deoxy-manno-octulosonate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)55,4992
Polymers55,4992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-20 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.928, 68.209, 71.476
Angle α, β, γ (deg.)82.73, 74.19, 76.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3-deoxy-manno-octulosonate cytidylyltransferase / / CMP-2-keto-3-deoxyoctulosonic acid synthase / CMP-KDO synthase / CKS


Mass: 27749.725 Da / Num. of mol.: 4 / Fragment: 3-deoxy-manno-octulosonate cytidylyltransferase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: kdsB, VC1875, VC_1875 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: Q9KQX2, 3-deoxy-manno-octulosonate cytidylyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1M tri-Na citrate, 0.1M sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.753→68.606 Å / Num. all: 172421 / Num. obs: 104474 / % possible obs: 94.42 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 1.2 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 22.75
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 1.96 / % possible all: 92.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1vic
Resolution: 1.75→25.06 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.131 / SU ML: 0.1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23209 4919 5 %RANDOM
Rwork0.19806 ---
obs0.19979 93730 100 %-
all-93730 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.235 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-1.05 Å20.56 Å2
2--0.36 Å2-1.6 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 1 690 8459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227979
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.95710898
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.81851014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87424.429359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86151295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3951556
X-RAY DIFFRACTIONr_chiral_restr0.0860.21247
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216124
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4751.55062
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88228214
X-RAY DIFFRACTIONr_scbond_it1.55732917
X-RAY DIFFRACTIONr_scangle_it2.6544.52680
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.753→1.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 351 -
Rwork0.287 6714 -
obs--100 %
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)
15.10891.9337-0.0439.54821.27064.4677-0.12610.2946-0.2186-0.0825-0.00790.1340.20310.04910.13410.17190.00310.02160.151-0.030.131646.960828.2512-14.379
23.03332.01170.99655.792.5787.092-0.16830.04560.3872-0.2178-0.22610.4908-0.2473-0.72980.39440.17880.0017-0.01930.0941-0.01520.233756.042346.4821-5.2978
33.2051.10630.15592.34730.28571.7796-0.13510.43120.0491-0.26320.0487-0.0896-0.09740.13490.08650.1802-0.00960.03980.17110.01170.073956.877534.9803-15.7941
47.67573.1434-0.44643.8924-1.11783.4370.9764-0.3581.13060.4331-1.00430.9192-0.6458-0.04680.02790.2596-0.0280.08110.411-0.20240.283441.730842.3289-14.3861
52.3453-0.42850.10591.7537-0.12541.6513-0.03250.2586-0.1178-0.2375-0.00130.126-0.1237-0.10750.03380.17320.00770.00130.1359-0.01610.148446.938928.3346-11.6186
62.0810.70620.70232.20361.17534.2591-0.0372-0.2158-0.20030.05440.1267-0.09170.02890.1656-0.08950.11370.03460.00660.15540.01630.193342.68523.47981.8328
71.91960.1293-0.6981.3302-0.05871.8550.0507-0.2853-0.03560.1336-0.0683-0.0357-0.00240.14710.01760.13010.0068-0.00360.17110.02030.156937.750227.811412.0824
81.84920.1286-0.43140.7748-0.07920.96280.0585-0.06150.01790.0231-0.0039-0.0169-0.22060.0696-0.05460.18590.0262-0.00330.1267-0.00750.174437.502730.82183.3396
92.1259-0.5218-0.61571.32410.60430.80320.03740.05020.0179-0.0358-0.020.0527-0.1166-0.0704-0.01740.1580.0235-0.00080.12630.03030.166134.760531.41150.6211
102.45280.42280.30152.5282-0.1780.27760.1029-0.1203-0.00380.012-0.0712-0.07960.01180.102-0.03170.1992-0.0047-0.01020.1262-0.00350.125264.396333.2682-0.4712
115.54580.21-0.13034.64961.8553.31590.18050.0146-0.19120.5142-0.0138-0.09450.50570.2053-0.16670.1615-0.0463-0.02060.2283-0.03350.11799.367118.745425.9644
121.897-0.11370.66244.4360.65267.34630.1269-0.1115-0.02910.5521-0.0210.19760.1999-0.239-0.10590.1024-0.06240.05380.2255-0.01290.08525.676722.820431.3534
133.0996-3.8486-3.07677.40890.1028.9786-0.2641-0.2095-0.36560.5056-0.23160.15480.51260.71470.49580.3895-0.1732-0.19440.26850.11930.23159.405112.475231.3523
142.15580.6001-0.78783.18041.2281.3421-0.00780.122-0.21170.14250.0637-0.00620.0717-0.1616-0.05590.086-0.02010.00220.2506-0.03110.12138.075419.467119.8193
152.42711.03510.49122.29070.42841.65580.0808-0.30350.0421-0.0542-0.1020.0094-0.1036-0.160.02120.1130.03190.02820.219-0.01680.139516.106431.400313.6894
161.94370.6382-0.15231.3790.12221.68170.1158-0.22640.18250.1364-0.0771-0.0028-0.1401-0.0252-0.03870.14380.02050.01460.1592-0.01410.145628.329436.40715.4221
1716.8594-11.9312-3.27549.8244.75975.01910.18210.2963-0.1837-0.0478-0.50450.22060.1036-0.45730.32240.0806-0.08030.02730.25710.16750.346116.998913.927112.9187
182.2852-0.1112-0.22521.48390.40061.43460.0135-0.142-0.32850.039-0.05080.03580.1035-0.02840.03730.1487-0.00520.02940.15510.04880.157924.879821.448313.4369
191.91680.5301-4.24917.2191-3.025911.78530.21950.10570.13360.6562-0.1312-0.6784-0.38290.5717-0.08840.2924-0.0342-0.02180.3850.01070.084913.699533.694734.3916
205.99390.2273-4.146844.0302-36.798139.76390.40350.14961.58820.41-0.197-0.7701-1.2612-1.1285-0.20640.59020.06540.19210.2954-0.03390.47853.756738.893236.5894
217.80884.43911.41298.68253.48523.8809-0.06710.04780.1942-0.18190.12780.3659-0.15130.0207-0.06070.1903-0.0330.0020.1813-0.00760.1156-21.5537-3.811519.2785
224.26340.8204-0.56264.74810.2761.03-0.0608-0.2504-0.16070.37510.08070.40160.06680.0222-0.01980.1603-0.0440.05940.16450.02250.0842-23.7233-11.153722.4743
236.33020.276-1.70119.3449-2.69372.5794-0.0674-0.09670.19950.22510.29671.0631-0.0982-0.3415-0.22930.0961-0.02970.1010.1763-0.03480.2504-31.7697-2.935621.6535
249.7917-2.17090.51269.08870.82275.699-0.285-0.1370.23410.21780.43380.1176-0.25610.0679-0.14870.1117-0.0010.01320.0499-0.05840.222-20.82726.672318.3222
253.87922.0457-0.6783.4968-0.03450.85650.0456-0.30590.02440.1341-0.0347-0.0510.02540.0648-0.01090.1543-0.039-0.02960.1776-0.02180.1052-9.9638-4.565319.8077
260.90970.4449-0.52051.41090.44851.7857-0.004-0.0593-0.10430.0039-0.0337-0.04910.19180.12420.03770.14330.0253-0.02580.09760.02140.1816-3.2282-8.97272.9439
273.6416-1.0962-3.31692.34662.46256.70290.05880.1178-0.3817-0.0958-0.1097-0.15540.29130.13440.05090.15680.0715-0.02870.05610.01020.1930.491-15.3345-0.7772
280.67960.33350.76727.1182-6.67858.05260.0245-0.18160.11990.0956-0.2856-0.0501-0.0437-0.09370.26110.05150.024-0.00630.2346-0.15840.2803-13.30078.466111.9374
291.2130.55310.2941.6996-0.10612.00830.0096-0.09560.10410.007-0.07530.1269-0.0647-0.14150.06570.11340.0277-0.00710.1093-0.00960.2004-8.64340.69955.4372
306.6808-0.32492.56824.6494-1.59089.0852-0.0329-0.017-0.7080.15740.0036-0.22760.30040.20930.02930.1336-0.040.03120.0823-0.02950.2571-21.7385-23.539517.0239
315.22920.5782-0.11440.5566-0.20797.4247-0.00450.24590.2441-0.00040.15520.178-0.2237-0.1359-0.15080.1981-0.11470.06730.1396-0.01040.139420.705414.4134-13.3423
3215.7025-5.7346-0.110222.4697-6.978715.48980.15351.1104-2.22341.00240.3757-1.85940.980.8722-0.52920.35330.0615-0.25640.2864-0.42760.847423.834-3.0234-25.3375
336.0166-1.7936-0.96664.34011.63154.4871-0.0780.77580.1489-0.130.091-0.3562-0.16160.5014-0.0130.1642-0.12950.06940.2553-0.0190.071323.518811.0441-21.8904
3415.7151-3.06920.30040.86622.018117.6669-0.6670.1864-1.17080.33640.13980.19821.68481.08790.52720.30150.00910.17220.2042-0.20110.558930.38083.5062-16.3526
354.17090.99322.73761.09911.33563.57570.06410.1369-0.0982-0.01450.0764-0.22340.25850.0463-0.14050.2066-0.0730.05410.13290.00280.08920.136711.2279-12.8234
362.02230.6702-0.10391.4787-0.57710.5863-0.10850.2192-0.0531-0.23530.16520.0492-0.05810.0438-0.05670.2283-0.0139-0.0110.1381-0.00780.14081.59114.0042-9.317
374.40762.3340.88072.25610.57951.4406-0.06590.1554-0.1812-0.25240.1103-0.0143-0.01070.0043-0.04440.2065-0.0015-0.03290.10870.00370.1380.26921.566-10.3849
389.466810.98893.145913.61975.83236.56480.2459-0.6933-0.66370.4433-0.1106-0.70420.43191.5831-0.13530.03140.0943-0.03710.64720.07240.295614.332-3.55571.1017
391.74770.0983-0.05193.1168-2.13824.75270.015-0.0803-0.125-0.0180.0516-0.1578-0.36930.3525-0.06660.1179-0.05030.01560.1521-0.03530.13558.19635.1489-3.6454
407.15-2.9074-0.40062.59721.805311.09220.28480.9816-0.62320.0297-0.25830.31140.1777-0.0723-0.02660.2279-0.10120.05640.298-0.15450.100312.3971.8856-31.2007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A10 - 19
3X-RAY DIFFRACTION3A20 - 65
4X-RAY DIFFRACTION4A66 - 83
5X-RAY DIFFRACTION5A84 - 111
6X-RAY DIFFRACTION6A112 - 134
7X-RAY DIFFRACTION7A135 - 166
8X-RAY DIFFRACTION8A167 - 203
9X-RAY DIFFRACTION9A204 - 228
10X-RAY DIFFRACTION10A229 - 252
11X-RAY DIFFRACTION11B1 - 13
12X-RAY DIFFRACTION12B14 - 51
13X-RAY DIFFRACTION13B52 - 78
14X-RAY DIFFRACTION14B79 - 110
15X-RAY DIFFRACTION15B111 - 134
16X-RAY DIFFRACTION16B135 - 184
17X-RAY DIFFRACTION17B185 - 198
18X-RAY DIFFRACTION18B199 - 228
19X-RAY DIFFRACTION19B229 - 243
20X-RAY DIFFRACTION20B244 - 251
21X-RAY DIFFRACTION21C1 - 13
22X-RAY DIFFRACTION22C14 - 49
23X-RAY DIFFRACTION23C50 - 72
24X-RAY DIFFRACTION24C73 - 92
25X-RAY DIFFRACTION25C93 - 123
26X-RAY DIFFRACTION26C124 - 163
27X-RAY DIFFRACTION27C164 - 184
28X-RAY DIFFRACTION28C185 - 199
29X-RAY DIFFRACTION29C200 - 231
30X-RAY DIFFRACTION30C232 - 251
31X-RAY DIFFRACTION31D1 - 8
32X-RAY DIFFRACTION32D9 - 26
33X-RAY DIFFRACTION33D27 - 51
34X-RAY DIFFRACTION34D52 - 79
35X-RAY DIFFRACTION35D80 - 110
36X-RAY DIFFRACTION36D111 - 163
37X-RAY DIFFRACTION37D164 - 193
38X-RAY DIFFRACTION38D194 - 208
39X-RAY DIFFRACTION39D209 - 228
40X-RAY DIFFRACTION40D229 - 250

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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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