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- PDB-4w9u: Crystal Structure of an Acyl-CoA dehydrogenase from Brucella meli... -

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Basic information

Entry
Database: PDB / ID: 4w9u
TitleCrystal Structure of an Acyl-CoA dehydrogenase from Brucella melitensis
ComponentsAcyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / NIAID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glutaryl-CoA dehydrogenase / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain ...Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Acyl-CoA dehydrogenase:Acyl-CoA dehydrogenase, C-terminal:Acyl-CoA dehydrogenase, central domain:Acyl-CoA dehydrogenase, N-te
Similarity search - Component
Biological speciesBrucella abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of an Acyl-CoA dehydrogenase from Brucella melitensis
Authors: Dranow, D.M. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA dehydrogenase
B: Acyl-CoA dehydrogenase
C: Acyl-CoA dehydrogenase
D: Acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,85410
Polymers173,4824
Non-polymers3726
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14550 Å2
ΔGint-46 kcal/mol
Surface area51450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.020, 106.660, 99.390
Angle α, β, γ (deg.)90.000, 108.120, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: PHE / End label comp-ID: PHE

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ARGARGchain AAA3 - 3944 - 395
2ARGARGchain BBB3 - 3944 - 395
3ALAALAchain CCC4 - 3945 - 395
4ALAALAchain DDD4 - 3945 - 395

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Components

#1: Protein
Acyl-CoA dehydrogenase /


Mass: 43370.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YPZ4*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG(D2): 30% PEG-400, 100mM HEPES free acid/ NaOH, 200mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 63306 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 30.31 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.091 / Χ2: 1.005 / Net I/σ(I): 13.88 / Num. measured all: 288458
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.4-2.464.60.8920.5572.5121649467246650.62999.9
2.46-2.530.920.4692.9721109456745520.5399.7
2.53-2.60.940.3963.4920670446344520.44799.8
2.6-2.680.9510.3334.1120023434543200.37799.4
2.68-2.770.9650.2844.8219133413141210.32199.8
2.77-2.870.9750.2395.7818807406640510.2799.6
2.87-2.980.9830.1797.7518158393339130.20299.5
2.98-3.10.9890.1529.1917292376237450.17299.5
3.1-3.240.9930.11511.4116725361836120.1399.8
3.24-3.390.9950.08914.7315789345134380.199.6
3.39-3.580.9960.07517.5314881331032860.08599.3
3.58-3.790.9960.06221.5612827310830080.07196.8
3.79-4.060.9980.04925.3812359292628580.05697.7
4.06-4.380.9980.0429.4112067271726960.04699.2
4.38-4.80.9980.03830.8611297254425290.04399.4
4.8-5.370.9980.03930.0510059228522700.04599.3
5.37-6.20.9980.04128.048600200620000.04799.7
6.2-7.590.9990.03333.457835172317190.03799.8
7.59-10.730.9990.02441.355974133613290.02799.5
10.730.9990.02442.1232047567420.02798.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX(phenix.refine: dev_1769)refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.23 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 2806 4.97 %Random selection
Rwork0.1797 53617 --
obs0.1827 56423 88.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.23 Å2 / Biso mean: 43.9655 Å2 / Biso min: 12.74 Å2
Refinement stepCycle: final / Resolution: 2.4→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10940 0 24 330 11294
Biso mean--52.42 36.16 -
Num. residues----1478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911183
X-RAY DIFFRACTIONf_angle_d1.17315107
X-RAY DIFFRACTIONf_chiral_restr0.0451664
X-RAY DIFFRACTIONf_plane_restr0.0061980
X-RAY DIFFRACTIONf_dihedral_angle_d12.1813972
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6561X-RAY DIFFRACTION7.987TORSIONAL
12B6561X-RAY DIFFRACTION7.987TORSIONAL
13C6561X-RAY DIFFRACTION7.987TORSIONAL
14D6561X-RAY DIFFRACTION7.987TORSIONAL
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 (%)
2.4001-2.44140.35011130.27112323243677
2.4414-2.48580.32311280.26142320244877
2.4858-2.53370.32531370.23982375251279
2.5337-2.58540.27111070.23032405251280
2.5854-2.64160.30041320.22162458259081
2.6416-2.7030.30741350.22132450258582
2.703-2.77060.27541330.21892461259482
2.7706-2.84550.29731520.22392503265583
2.8455-2.92920.3511320.21332606273886
2.9292-3.02380.26551470.20512615276287
3.0238-3.13180.26851440.20372703284789
3.1318-3.25720.25251300.19622827295793
3.2572-3.40540.26031400.19332879301995
3.4054-3.58490.23381460.18662896304296
3.5849-3.80940.24181730.16822814298794
3.8094-4.10330.19661420.14342904304695
4.1033-4.5160.1831540.12552958311297
4.516-5.16880.18681350.1373018315399
5.1688-6.50940.21661620.17293009317199
6.5094-47.23960.19081640.161630933257100
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)
12.20991.2890.85082.52470.77823.8549-0.2137-0.38190.21840.25840.1843-0.3391-0.3066-0.3493-0.07230.32070.05720.01050.2345-0.08440.397220.049372.098249.8983
22.68540.74240.05892.6381-0.34743.60620.3048-0.2842-0.24970.74250.033-0.53470.2290.4286-0.19040.48320.0739-0.21760.3604-0.14020.501530.125762.688259.3029
31.9345-0.55611.08750.34440.07981.64860.2791-0.3337-0.50930.60340.1753-0.60290.15210.0167-0.20740.61250.0717-0.23930.4373-0.08920.46528.302754.283160.1929
41.41950.42930.620.68670.40641.80050.2727-0.5032-0.88820.4625-0.1303-0.83570.35130.0424-0.2620.95120.0821-0.44530.5639-0.00940.687733.046444.18568.0078
50.4317-0.6019-0.18841.02820.6040.70810.0006-0.5681-0.53130.36620.20260.21820.9256-0.1265-0.21761.33620.1323-0.67710.4650.23840.851227.981838.252670.4875
62.87990.7682-0.13210.2145-0.20951.82530.0104-0.2752-1.03010.36580.2123-0.74230.9366-0.0001-0.22360.97280.2075-0.55210.55560.120.828135.504340.96768.2798
71.34690.02250.35941.4405-1.04423.14090.1557-0.2011-0.07980.2387-0.0204-0.32790.14320.5888-0.13050.39040.0264-0.07580.2693-0.120.404923.898658.22946.1936
80.62950.0493-0.66981.3311-0.05552.5253-0.0156-0.0062-0.03420.03460.0856-0.23330.12980.053-0.11320.29590.0095-0.06560.2788-0.07280.323418.508259.000539.6192
93.8140.0037-0.29272.0975-2.94377.35130.49240.39490.0695-0.37330.3605-0.38541.27420.2002-0.29510.41830.1989-0.12240.6444-0.29680.511731.765154.705339.3853
102.2721.2002-2.46067.8094-0.69166.15740.0253-0.1981-0.413-0.1327-0.0823-0.7296-0.36810.12230.00330.45440.0108-0.07770.24170.00910.316512.993138.825247.6213
111.7348-0.65690.69561.5112-0.73491.3976-0.0578-0.2405-0.0530.27180.10850.2321-0.1505-0.2507-0.08710.26570.02330.08450.3592-0.00250.2919-12.118464.90840.622
123.77930.99990.19045.4314-0.05933.491-0.08730.30420.2515-0.15810.1184-0.1161-0.3772-0.1425-0.01570.27490.02670.0540.31350.04880.2908-13.481179.049920.5288
131.1547-0.3478-0.08361.4062-0.31210.34560.0491-0.0023-0.1047-0.0520.04310.10430.028-0.1116-0.09770.2116-0.00270.01760.2946-0.00540.24181.572453.834536.5533
143.1338-0.15080.20633.180.86042.4342-0.11690.0537-0.0586-0.37830.10670.2065-0.10150.0387-0.13720.43620.030.02420.2189-0.02350.370512.246769.42225.2105
152.86292.19311.28463.2064-0.03730.91510.18960.153-0.0518-0.4013-0.02710.28070.2298-0.061-0.03980.44970.009-0.14630.2738-0.03990.30285.815133.63820.6855
161.82170.57280.63361.67320.30740.91640.2681-0.3453-0.4729-0.07420.04410.30060.5876-0.4658-0.12650.5176-0.1784-0.1780.45060.07490.5921-4.344618.70412.4992
170.0409-0.34640.02343.3343-0.41570.88440.1713-0.6511-0.75310.59330.01350.63570.4059-0.8281-0.32060.5853-0.2638-0.17680.54710.31520.8197-8.028113.859818.0505
181.27530.32620.32283.18020.28492.05620.1955-0.5465-0.70880.624-0.07590.43750.9532-0.7308-0.28580.7191-0.2669-0.14180.61390.2280.8148-7.210411.948618.0567
190.71280.37350.1062.64870.23210.74490.09340.04340.0367-0.1188-0.06410.2169-0.0035-0.1488-0.02010.24110.0036-0.02940.2528-0.02350.24211.785542.016813.803
204.7735-0.2189-0.12647.5774-2.45785.05250.1686-0.1480.14210.0458-0.38241.12940.4555-0.83750.44520.31-0.08460.02030.6196-0.1640.47660.256345.361217.0965
216.6294-0.1669-1.84464.56741.25583.29750.20660.09260.2232-0.0202-0.12220.26070.0325-0.1954-0.08750.2989-0.044-0.04120.2090.01580.386312.867627.774730.3937
222.28080.9319-0.78061.4489-0.62421.37830.03170.0605-0.4226-0.2477-0.0073-0.32150.26320.1764-0.00630.29440.0782-0.01250.2643-0.06170.370244.449137.438613.1802
232.71441.2123-1.2574.4769-3.35093.690.15480.04620.4983-0.02510.08150.3223-0.2443-0.0287-0.21690.2810.06370.0260.2811-0.00810.282951.095263.45737.6022
244.1641-0.1911.89583.2563-1.93315.9811-0.09510.17240.2158-0.05460.08940.1048-0.1395-0.20340.16060.24180.06530.04920.3233-0.04180.278150.512560.10447.4946
253.47591.18830.54033.9731-0.40743.9980.0153-0.1351-0.05150.1023-0.20440.0949-0.32560.0860.20540.2060.05470.06520.266-0.01910.303453.719259.118611.6907
260.8180.1451-0.2261.0391-0.75971.85980.0925-0.0262-0.0549-0.00770.02130.00180.10910.1845-0.03880.23820.0115-0.03260.2198-0.02990.306728.570439.515422.2499
279.55381.5713-4.32033.95350.06339.53680.3129-0.99450.4220.34690.3406-0.6428-0.18060.6655-0.57710.27090.0031-0.03680.3851-0.11860.453235.440845.037631.4055
289.2503-0.91534.00146.3233-0.55822.70050.29160.25450.171-0.54970.0102-0.60210.020.7754-0.1660.3390.0140.07530.2926-0.03850.385824.947258.627412.3568
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 35 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 90 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 91 through 116 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 177 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 178 through 198 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 241 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 242 through 277 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 278 through 347 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 348 through 371 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 372 through 394 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 129 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 130 through 241 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 242 through 371 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 372 through 394 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 4 through 90 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 91 through 177 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 178 through 218 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 219 through 242 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 243 through 347 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 348 through 371 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 372 through 394 )C0
22X-RAY DIFFRACTION22chain 'D' and (resid 4 through 129 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 130 through 167 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 168 through 198 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 199 through 242 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 243 through 347 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 348 through 371 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 372 through 394 )D0

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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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