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Basic information

Entry
Database: PDB / ID: 5aji
TitleMscS D67R1 high resolution
ComponentsSMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


intracellular water homeostasis / mechanosensitive monoatomic ion channel activity / monoatomic ion transmembrane transport / protein homooligomerization / identical protein binding / membrane / plasma membrane
Similarity search - Function
Helix Hairpins - #1260 / SH3 type barrels. - #60 / Mechanosensitive ion channel MscS, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site ...Helix Hairpins - #1260 / SH3 type barrels. - #60 / Mechanosensitive ion channel MscS, archaea/bacteria type / Conserved TM helix / Mechanosensitive ion channel, conserved TM helix / : / : / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel, transmembrane helices 2/3 / Mechanosensitive ion channel MscS, conserved site / Uncharacterized protein family UPF0003 signature. / Mechanosensitive ion channel MscS, C-terminal / Mechanosensitive ion channel MscS, transmembrane-2 / Mechanosensitive ion channel MscS / Mechanosensitive ion channel, beta-domain / Mechanosensitive ion channel MscS, beta-domain superfamily / Alpha-Beta Plaits - #100 / LSM domain superfamily / SH3 type barrels. / Helix Hairpins / Roll / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DECANE / HEXANE / N-OCTANE / Small-conductance mechanosensitive channel / Small-conductance mechanosensitive channel
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsNaismith, J.H. / Pliotas, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The Role of Lipids in Mechanosensation.
Authors: Pliotas, C. / Dahl, A.C.E. / Rasmussen, T. / Mahendran, K.R. / Smith, T.K. / Marius, P. / Gault, J. / Banda, T. / Rasmussen, A. / Miller, S. / Robinson, C.V. / Bayley, H. / Sansom, M.S.P. / ...Authors: Pliotas, C. / Dahl, A.C.E. / Rasmussen, T. / Mahendran, K.R. / Smith, T.K. / Marius, P. / Gault, J. / Banda, T. / Rasmussen, A. / Miller, S. / Robinson, C.V. / Bayley, H. / Sansom, M.S.P. / Booth, I.R. / Naismith, J.H.
History
DepositionFeb 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 23, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 35-STRANDED BARREL THIS IS REPRESENTED BY A 36-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
B: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
C: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
D: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
E: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
F: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
G: SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,18422
Polymers217,6677
Non-polymers1,51715
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33600 Å2
ΔGint-185 kcal/mol
Surface area86330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.330, 149.090, 173.820
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
SMALL-CONDUCTANCE MECHANOSENSITIVE CHANNEL / MSCS


Mass: 31095.234 Da / Num. of mol.: 7 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN IS SPIN LABELED ON D67C. / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C0S2, UniProt: P0C0S1*PLUS
#2: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18
#3: Chemical
ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14
#4: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22

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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: 3.76 Å3/Da / Density % sol: 67.29 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorDate: Jan 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.99→64 Å / Num. obs: 66747 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 6.7
Reflection shellResolution: 2.99→3.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.002 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AGE
Resolution: 2.99→68.51 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.911 / SU B: 50.987 / SU ML: 0.373 / Cross valid method: THROUGHOUT / ESU R: 1.017 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED A HIGHER RESOLUTION VERSION OF 4AGE
RfactorNum. reflection% reflectionSelection details
Rfree0.26331 3401 5.1 %RANDOM
Rwork0.24446 ---
obs0.2454 63346 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.531 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--2.88 Å20 Å2
3----3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.99→68.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13859 0 104 0 13963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914130
X-RAY DIFFRACTIONr_bond_other_d0.0040.0214603
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.97619143
X-RAY DIFFRACTIONr_angle_other_deg1.003333172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.39551802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2723.16557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.035152415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.62915124
X-RAY DIFFRACTIONr_chiral_restr0.0590.22340
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215867
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023227
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_it1.2094.767229
X-RAY DIFFRACTIONr_mcbond_other1.2094.767228
X-RAY DIFFRACTIONr_mcangle_it2.0887.1399024
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4315.0766901
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 252 -
Rwork0.399 4622 -
obs--99.98 %
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)
12.4619-0.37370.77210.25383.31274.1490.10141.0511-0.2461-0.92450.0198-0.16380.0488-0.0311-0.12121.6008-0.17530.03141.43310.17090.4952-13.4275.461-21.321
245.8087-8.218414.03651.489-2.52374.3211-0.70440.76082.26810.146-0.0387-0.4187-0.41010.2730.74311.8585-0.6016-0.22570.82490.44471.0849-4.60727.395-0.76
30.4533-1.17340.62467.88283.12595.87310.05450.35280.1664-0.7904-0.4315-0.416-0.32070.45440.3771.2675-0.2236-0.16381.14870.10650.466-13.8897.343-6.968
48.19640.6121.69031.17240.62882.933-0.28850.4110.8129-0.51550.0706-0.4221-0.40360.16370.21780.7201-0.0668-0.06140.15970.14560.64966.64416.13417.906
51.550.21530.46042.4491-0.65133.2989-0.2257-0.23620.53850.3719-0.1065-0.7878-0.42130.03630.33220.8094-0.1436-0.39640.078-0.03791.116621.0626.54450.699
66.9593-4.7857-1.78217.7687-2.47893.54630.7242.16150.2389-1.3303-0.62730.10820.6056-1.1924-0.09672.2199-0.3861-0.58671.51130.59011.2717-24.5923.111-15.007
74.46011.90249.97972.67444.493923.6228-0.63440.2110.7033-0.24710.23690.2944-1.2616-0.01390.39741.19530.0429-0.32870.48050.31421.3391-23.98329.83112.057
84.68620.1369-0.4790.1857-0.95.9468-0.14391.38550.6325-0.26920.05470.12460.5001-0.45910.08921.2249-0.1817-0.3840.72970.13020.562-21.77114.228-1.697
95.6060.98962.26585.57812.14836.135-0.03830.03930.3136-0.0574-0.2240.2461-0.4369-0.17310.26230.59730.0351-0.18050.0246-0.02060.5655-9.31424.22431.694
101.8021-0.13650.94491.83490.03382.1809-0.1375-0.51270.36520.604-0.0091-0.2027-0.2065-0.25080.14660.9529-0.0222-0.27510.1572-0.14950.66633.38421.23858.249
117.0041-2.8334-0.22658.6518-2.1850.70610.11120.87311.1164-0.25590.30090.9895-0.0005-0.2848-0.4121.25570.339-0.58340.90950.14791.1374-42.14925.943.177
122.5602-1.65524.22687.65751.21679.4798-0.5866-0.57470.52320.3024-0.25360.2095-1.0176-1.35640.84020.88910.3957-0.20771.0817-0.03411.0934-39.39516.27128.1
133.6991-0.5177-0.09123.4846-3.48369.9808-0.03680.74781.1046-0.6776-0.20970.2223-0.0308-0.52230.24650.95130.0265-0.38370.34610.08930.7913-30.46514.95310.288
143.48272.9582.89097.26252.62964.85570.1947-0.53050.24560.7255-0.21170.2033-0.1407-0.92040.01710.67280.0286-0.08570.2973-0.08290.4506-18.45112.4344.833
154.2429-1.4254-0.26342.91170.2371.3718-0.0386-0.742-0.04870.78260.0316-0.04420.0631-0.27450.0071.1886-0.0663-0.20990.56230.01040.3327-0.766-0.20771.727
163.47352.59861.15397.6567-2.27792.7990.25470.80670.3809-0.43850.16821.8524-0.216-0.071-0.42290.87590.4622-0.21691.57660.07761.3405-55.83811.89911.661
179.2191-4.88112.50234.7751-4.052210.0086-0.4621-0.90580.25710.34320.61220.39010.0513-1.972-0.15020.6662-0.1448-0.17541.08560.13970.7931-41.829-8.84729.852
180.1269-0.22690.46074.9878-1.63582.5030.0211-0.04830.2106-0.4082-0.27730.6467-0.1062-0.42810.25620.87070.2512-0.2720.79080.11920.9303-38.8235.52714.464
192.9791-0.24221.5663.70813.32828.1196-0.0447-0.4968-0.17940.6751-0.02170.49630.5445-0.63630.06640.605-0.0965-0.04280.27280.09670.4819-19.448-7.85644.962
205.09820.98930.93143.3246-0.36662.07830.1291-0.7563-0.4850.7334-0.0995-0.45260.3247-0.1369-0.02960.9894-0.0458-0.27170.33090.22550.53717.605-20.00864.567
210.78940.8076-0.3693.85652.85983.6425-0.03850.13920.1071-0.2989-0.53030.7324-0.2043-0.90160.56880.6822-0.2876-0.23531.38320.18511.3913-55.412-12.53811.755
2210.5146-6.77322.98846.6815-2.47674.28310.3307-0.3665-0.68270.1112-0.17180.4650.5877-0.7035-0.15880.8235-0.2423-0.350.43530.16830.7563-32.848-22.55315.237
232.1265-0.22230.9311.2607-1.17543.36760.13340.0183-0.3257-0.0645-0.12270.13060.4453-0.0511-0.01060.5834-0.0441-0.14160.10850.08290.5312-12.824-18.69831.977
243.15161.10671.43763.46920.82412.41210.1106-0.0415-0.35460.157-0.0425-0.80160.34070.2178-0.06810.66990.0552-0.2720.0760.19180.983222.675-26.16548.137
2561.135586.412899.7133335.576877.5431181.4689-2.60764.9454-1.48449.43037.56216.6758-8.14317.9239-4.95451.09660.08270.4861.759-0.52023.006537.4817.23364.598
269.50732.3712.83122.64890.0142.2250.42620.5554-1.4606-0.61730.0799-0.04480.72710.1154-0.50611.12320.0321-0.28780.6227-0.33130.9852-19.04-25.959-0.708
2718.4733-2.4372-7.33415.3651-0.79263.6673-0.40580.9737-0.6865-0.510.29210.37330.6096-0.64160.11370.958-0.1406-0.43890.696-0.09130.7845-29.08-18.3121.255
2819.93541.00482.6030.56370.38680.6981-0.13310.6679-0.4965-0.40980.05750.21860.12790.0820.07560.8418-0.0269-0.11570.48230.0140.5628-10.309-15.03613.857
294.9085-2.03212.60863.9017-4.56965.58220.18420.7517-0.4739-0.1851-0.5307-0.49040.42080.74390.34660.63010.0627-0.01880.27240.05730.74988.653-19.3123.328
302.21290.00051.03583.85831.6373.81970.0890.35590.0409-0.0171-0.0205-1.09860.24030.531-0.06860.42470.0143-0.08470.27920.17011.283336.323-8.67738.198
3110.39766.07022.82235.59742.14616.0881-0.15772.3282-1.0637-1.27150.5037-0.74790.2551.0872-0.3461.44690.13580.07721.4052-0.19910.5887-7.335-9.337-13.486
326.00073.6192.58364.97712.07553.4027-0.08021.1218-0.1581-0.93590.13690.41940.56220.3582-0.05670.9726-0.0321-0.12080.7526-0.15960.5652-15.709-9.593-4.415
336.366-2.93632.97168.0106-0.81012.9609-0.21290.70830.4237-0.7056-0.2541-1.13220.2780.38130.4670.7022-0.06940.18860.33870.11940.637912.981-1.52914.318
343.2124-0.1940.81913.33070.74714.5672-0.09870.44420.6077-0.349-0.1128-1.0383-0.52010.57510.21140.5803-0.2336-0.04570.23510.23291.337134.09415.64232.758
357.5708-0.0419-4.58152.18552.751112.8655-0.3182-0.18290.18630.24140.2247-0.81740.06990.78770.09350.4469-0.0633-0.36310.31560.14891.296837.4979.30949.894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 51
2X-RAY DIFFRACTION2A52 - 64
3X-RAY DIFFRACTION3A65 - 104
4X-RAY DIFFRACTION4A105 - 178
5X-RAY DIFFRACTION5A179 - 281
6X-RAY DIFFRACTION6B25 - 42
7X-RAY DIFFRACTION7B43 - 76
8X-RAY DIFFRACTION8B77 - 111
9X-RAY DIFFRACTION9B112 - 148
10X-RAY DIFFRACTION10B149 - 279
11X-RAY DIFFRACTION11C25 - 45
12X-RAY DIFFRACTION12C46 - 76
13X-RAY DIFFRACTION13C77 - 116
14X-RAY DIFFRACTION14C117 - 180
15X-RAY DIFFRACTION15C181 - 279
16X-RAY DIFFRACTION16D17 - 43
17X-RAY DIFFRACTION17D44 - 77
18X-RAY DIFFRACTION18D78 - 111
19X-RAY DIFFRACTION19D112 - 180
20X-RAY DIFFRACTION20D181 - 279
21X-RAY DIFFRACTION21E17 - 43
22X-RAY DIFFRACTION22E44 - 92
23X-RAY DIFFRACTION23E93 - 179
24X-RAY DIFFRACTION24E180 - 274
25X-RAY DIFFRACTION25E275 - 278
26X-RAY DIFFRACTION26F25 - 72
27X-RAY DIFFRACTION27F73 - 97
28X-RAY DIFFRACTION28F98 - 127
29X-RAY DIFFRACTION29F128 - 181
30X-RAY DIFFRACTION30F182 - 280
31X-RAY DIFFRACTION31G25 - 66
32X-RAY DIFFRACTION32G68 - 110
33X-RAY DIFFRACTION33G111 - 179
34X-RAY DIFFRACTION34G180 - 254
35X-RAY DIFFRACTION35G255 - 278

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  • 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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