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- PDB-4ycs: Crystal structure of putative lipoprotein from Peptoclostridium d... -

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Basic information

Entry
Database: PDB / ID: 4ycs
TitleCrystal structure of putative lipoprotein from Peptoclostridium difficile 630 (fragment)
ComponentsUncharacterized protein
KeywordsHYDROLASE / Human Microbiome / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


ABC transporter substrate-binding protein PnrA-like / ABC transporter substrate-binding protein PnrA-like / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Putative lipoprotein
Similarity search - Component
Biological speciesPeptoclostridium difficile 630 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsMichalska, K. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: Crystal structure of putative lipoprotein from Peptoclostridium difficile 630 (fragment)
Authors: Michalska, K. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionFeb 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,78811
Polymers85,4306
Non-polymers3585
Water6,359353
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3302
Polymers14,2381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,2381
Polymers14,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3302
Polymers14,2381
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4124
Polymers14,2381
Non-polymers1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,2381
Polymers14,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,2381
Polymers14,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.755, 119.501, 185.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biomolecule is unknown

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Components

#1: Protein
Uncharacterized protein / lipoprotein / fragment


Mass: 14238.272 Da / Num. of mol.: 6 / Fragment: UNP residues 45-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile 630 (bacteria)
Gene: BG47_10265 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: A0A031WBX8, UniProt: Q189B5*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.09 M Malonic Acid, 0.013 M Ammonium Citrate Tribasic, 0.006 M Succinic Acid, 0.015 M DL-Malic Acid, 0.02 M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, 0.1 M ...Details: 0.09 M Malonic Acid, 0.013 M Ammonium Citrate Tribasic, 0.006 M Succinic Acid, 0.015 M DL-Malic Acid, 0.02 M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, 0.1 M HEPES:NaOH pH 7.0, 10% (w/v) PEG MME 5000, cryo 25% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2013 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.98→30 Å / Num. obs: 57544 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 12.4
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.25 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 1.98→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.615 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22628 1077 1.9 %THIN SHELLS
Rwork0.17981 ---
obs0.18067 56177 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.857 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.98→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 23 353 6052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.025821
X-RAY DIFFRACTIONr_bond_other_d0.0020.025589
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9917853
X-RAY DIFFRACTIONr_angle_other_deg0.802312942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6695741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.24427.481262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.312151022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.16156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026695
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021191
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_it2.2442.312965
X-RAY DIFFRACTIONr_mcbond_other2.2342.3072963
X-RAY DIFFRACTIONr_mcangle_it3.3873.4383705
X-RAY DIFFRACTIONr_mcangle_other3.3883.4393706
X-RAY DIFFRACTIONr_scbond_it3.892.8622856
X-RAY DIFFRACTIONr_scbond_other3.892.8622856
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0854.054149
X-RAY DIFFRACTIONr_long_range_B_refined8.01319.796510
X-RAY DIFFRACTIONr_long_range_B_other8.01319.796510
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.982→2.033 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 54 -
Rwork0.253 3836 -
obs--90.61 %
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)
10.058-0.088-0.41080.29331.41437.95340.0116-0.0283-0.07190.05260.0987-0.01410.42920.0523-0.11030.1393-0.0331-0.030.18290.00210.1984-0.642681.525816.4717
21.3618-0.6644-0.18790.95420.38741.7337-0.157-0.0678-0.3861-0.06660.19890.36140.3566-0.1001-0.04180.208-0.0468-0.02550.12180.06410.20630.131776.499419.0979
31.024-0.2126-0.00612.57910.90061.4567-0.040.07710.0102-0.3569-0.02850.0101-0.14690.03250.06860.157-0.02-0.00450.13640.01430.06741.256889.082712.4678
40.7532-1.9269-0.71625.9823.35733.2644-0.04140.1140.2356-0.14470.0619-0.5507-0.14560.3483-0.02050.1413-0.10230.03320.17660.02270.13217.892691.689214.3586
53.6247-1.68671.4590.7996-0.76031.04050.45380.28980.1163-0.2414-0.19920.00010.34490.4655-0.25460.17910.1304-0.05670.3232-0.22140.23513.120581.430514.1395
610.2044-4.67211.8422.40730.56937.7938-0.1279-0.18010.06440.03540.0674-0.0104-0.1537-0.11980.06050.0617-0.0050.00520.0625-0.01260.168210.074882.09526.005
70.1858-0.65770.62584.0175-3.90723.80710.0375-0.01770.10520.27320.02520.037-0.2666-0.0037-0.06270.1839-0.03040.05810.17310.01280.206214.576347.1726-9.1732
82.4012-0.09040.00832.8357-1.78111.16980.3084-0.23260.38930.1331-0.05330.3373-0.10540.1545-0.25510.1304-0.06490.07580.2899-0.12330.158812.119751.7363-2.6547
90.65420.9331-0.53053.1384-0.37761.3060.015-0.0520.0963-0.33910.0227-0.04410.15540.0904-0.03770.1586-0.00750.04140.12250.00920.080614.522442.6216-15.1544
101.51130.7093-0.77423.8577-1.51910.7868-0.05290.22220.0541-0.37330.17180.36660.1713-0.1411-0.11890.1886-0.0452-0.07580.10190.00240.144.602937.9613-15.9314
113.5484-1.44921.24452.91732.5724.52260.2199-0.02730.0114-0.3854-0.0374-0.1489-0.3451-0.1112-0.18240.14280.02150.02910.13790.09070.1451.788751.9388-10.9872
125.8888-3.2776-4.25878.50941.29863.25540.0365-0.11570.3589-0.27150.212-0.35590.02310.0544-0.24850.0586-0.01920.01070.14710.02870.13633.427846.5273-1.6021
130.3904-1.0519-0.81013.69474.045.79350.07670.08850.0653-0.3641-0.1374-0.1007-0.5322-0.10640.06060.1466-0.00750.01620.2008-0.01370.114623.137849.97218.3691
140.713-0.8511-1.01665.8715.28727.0811-0.1290.19380.2336-0.11160.1391-0.1145-0.2168-0.0223-0.01010.1225-0.0723-0.01950.12090.05060.129625.951155.29711.5293
150.90380.215-0.07290.0565-0.0261.42-0.04840.1615-0.00530.01510.048-0.0012-0.0321-0.03450.00050.1507-0.00230.01410.153-0.01380.092823.29545.717611.2592
160.4395-0.85080.38324.57070.3081.2286-0.024-0.07570.04260.09610.051-0.17280.1420.2607-0.0270.09270.0714-0.00470.2814-0.02570.113131.586942.853416.5822
170.3003-0.227-1.00080.18750.77313.3610.0943-0.15340.0659-0.06670.1629-0.0658-0.29060.5435-0.25730.032-0.05330.00450.2073-0.05070.173837.605750.78912.1541
187.41171.8737-3.30191.05780.32383.79810.17140.09620.05950.16130.0265-0.03690.1359-0.0613-0.19780.06240.00490.01630.16070.0610.168734.657746.88970.6353
190.15560.07350.56930.28261.05274.61220.1409-0.02450.0548-0.1801-0.0554-0.0913-0.3174-0.3962-0.08550.33090.02750.1150.2055-0.05020.212329.534648.226555.8702
206.7098-0.872-2.05892.63193.15543.9772-0.0015-0.53280.2442-0.2885-0.0087-0.0133-0.4090.09570.01020.29330.007-0.13820.08450.02640.132328.948165.92158.1041
210.43290.0414-0.37010.83510.72431.8961-0.01310.02350.00820.0059-0.0108-0.0169-0.1264-0.16130.02390.08170.0176-0.01540.1386-0.02120.111629.585651.964158.9781
221.47571.3481-1.16324.212-0.630.9838-0.0157-0.05640.09360.13220.1198-0.02730.03110.0545-0.1040.07580.0339-0.04940.1192-0.01940.130736.700148.68367.34
230.4912-0.1804-0.91952.9121.1471.97410.1484-0.02880.072-0.32490.0921-0.2139-0.33060.0622-0.24040.1395-0.0212-0.03090.089-0.03970.189642.742455.185861.2177
243.48611.8314-1.72177.9288-0.79142.964-0.07480.0555-0.14310.22340.2946-0.1081-0.0363-0.2027-0.21980.0290.00770.00330.1296-0.0370.127839.736248.816651.1622
250.1830.0544-0.16380.0418-0.07010.167-0.0001-0.0310.0561-0.04750.06220.02810.0306-0.0305-0.06220.2113-0.02960.00760.21010.00450.133518.900750.846341.8437
260.72170.38571.97820.47721.28355.6310.0216-0.0897-0.0366-0.11320.202-0.1427-0.0055-0.0166-0.22350.1218-0.08110.02990.2833-0.10360.105519.860147.933949.729
271.13530.5042-0.1920.7048-0.99572.0011-0.0213-0.1135-0.0352-0.1255-0.04250.02770.10270.04740.06380.1731-0.0017-0.01950.1040.010.123519.333839.24837.9919
282.30391.0652-0.48449.2098-6.36196.29560.11870.3193-0.0673-0.3274-0.0569-0.06020.45410.0031-0.06180.1343-0.0416-0.02390.10170.00850.094912.489533.634334.0331
290.8712-0.41090.03780.3454-0.6042.4891-0.09110.0583-0.0538-0.00990.03530.06180.1919-0.23190.05580.0756-0.0686-0.02430.1480.030.19148.103637.44938.9109
303.8866-1.7486-2.08071.4192.4254.62380.3536-0.08910.3779-0.1036-0.0614-0.2171-0.0592-0.2193-0.29220.0373-0.0290.03480.1104-0.01140.18648.150950.252944.2873
310.3333-1.32020.74235.3425-2.99331.70470.12060.0758-0.0006-0.3616-0.2014-0.00610.21390.14710.08080.16760.02310.02110.16810.02850.184428.532374.415232.2418
320.78140.46310.47044.4955-0.21290.41060.02960.08120.1043-0.1952-0.13670.17760.10050.14460.10710.13750.03830.04180.14560.02240.12125.614872.961825.0699
330.7171-0.68820.74083.1271-0.42880.81-0.03550.0280.10130.2001-0.0561-0.11720.00860.00260.09160.14390.00250.00080.102-0.00640.108930.015476.657138.4199
340.58350.1851-0.54823.24491.48161.383-0.03940.0162-0.03450.4638-0.15110.23550.2829-0.10770.19050.2078-0.01380.06730.0544-0.04260.134221.585476.293242.9435
350.0457-0.38410.17323.275-1.43910.665-0.0069-0.0137-0.02230.11290.0450.28350.0041-0.0789-0.03810.141-0.07980.16360.1148-0.14760.25214.172374.522340.4747
360.05260.31660.10498.64880.04851.1371-0.03850.04420.0283-0.00760.0537-0.06780.0740.1253-0.01520.0948-0.0144-0.01680.08520.00640.142316.481574.886426.6429
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 61
2X-RAY DIFFRACTION2A62 - 91
3X-RAY DIFFRACTION3A92 - 122
4X-RAY DIFFRACTION4A123 - 139
5X-RAY DIFFRACTION5A140 - 162
6X-RAY DIFFRACTION6A163 - 169
7X-RAY DIFFRACTION7B47 - 61
8X-RAY DIFFRACTION8B62 - 85
9X-RAY DIFFRACTION9B86 - 121
10X-RAY DIFFRACTION10B122 - 146
11X-RAY DIFFRACTION11B147 - 157
12X-RAY DIFFRACTION12B158 - 169
13X-RAY DIFFRACTION13C48 - 61
14X-RAY DIFFRACTION14C62 - 79
15X-RAY DIFFRACTION15C80 - 117
16X-RAY DIFFRACTION16C118 - 138
17X-RAY DIFFRACTION17C139 - 157
18X-RAY DIFFRACTION18C158 - 169
19X-RAY DIFFRACTION19D48 - 56
20X-RAY DIFFRACTION20D57 - 67
21X-RAY DIFFRACTION21D68 - 121
22X-RAY DIFFRACTION22D122 - 139
23X-RAY DIFFRACTION23D140 - 157
24X-RAY DIFFRACTION24D158 - 169
25X-RAY DIFFRACTION25E48 - 78
26X-RAY DIFFRACTION26E79 - 88
27X-RAY DIFFRACTION27E89 - 118
28X-RAY DIFFRACTION28E119 - 126
29X-RAY DIFFRACTION29E127 - 147
30X-RAY DIFFRACTION30E148 - 169
31X-RAY DIFFRACTION31F48 - 60
32X-RAY DIFFRACTION32F61 - 85
33X-RAY DIFFRACTION33F86 - 113
34X-RAY DIFFRACTION34F114 - 139
35X-RAY DIFFRACTION35F140 - 152
36X-RAY DIFFRACTION36F153 - 169

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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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