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- PDB-2odr: Methanococcus Maripaludis Phosphoseryl-tRNA synthetase -

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Basic information

Entry
Database: PDB / ID: 2odr
TitleMethanococcus Maripaludis Phosphoseryl-tRNA synthetase
Components(phosphoseryl-tRNA synthetaseO-phospho-L-serine—tRNA ligase) x 4
KeywordsLIGASE / phosphoserine tRNA synthetase class II
Function / homology
Function and homology information


O-phospho-L-serine-tRNA ligase / phosphoserine-tRNA(Cys) ligase activity / tRNA aminoacylation / tRNA binding / translation / ATP binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3340 / Double Stranded RNA Binding Domain - #20 / O-phosphoseryl-tRNA(Cys) ligase / O-phosphoserine--tRNA(Cys) ligase, C-terminal domain / O-phosphoseryl-tRNA synthetase C-terminal domain / Double Stranded RNA Binding Domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Other non-globular / Bira Bifunctional Protein; Domain 2 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3340 / Double Stranded RNA Binding Domain - #20 / O-phosphoseryl-tRNA(Cys) ligase / O-phosphoserine--tRNA(Cys) ligase, C-terminal domain / O-phosphoseryl-tRNA synthetase C-terminal domain / Double Stranded RNA Binding Domain / Phenylalanyl-tRNA synthetase / tRNA synthetases class II core domain (F) / Other non-globular / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
O-phosphoserine--tRNA(Cys) ligase
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.228 Å
AuthorsSteitz, T.A. / Kamtekar, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Toward understanding phosphoseryl-tRNACys formation: the crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase.
Authors: Kamtekar, S. / Hohn, M.J. / Park, H.S. / Schnitzbauer, M. / Sauerwald, A. / Soll, D. / Steitz, T.A.
History
DepositionDec 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999SEQUENCE THE INSERTED AND C-TERMINAL DOMAINS OF THE SYNTHETASE ARE PARTIALLY DISORDERED. MANY OF ...SEQUENCE THE INSERTED AND C-TERMINAL DOMAINS OF THE SYNTHETASE ARE PARTIALLY DISORDERED. MANY OF THE RESIDUES IN THESE DOMAINS CANNOT BE ASSIGNED AND ARE LISTED AS UNK RESIDUES IN THE COORDINATES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: phosphoseryl-tRNA synthetase
B: phosphoseryl-tRNA synthetase
C: phosphoseryl-tRNA synthetase
D: phosphoseryl-tRNA synthetase


Theoretical massNumber of molelcules
Total (without water)293,7354
Polymers293,7354
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22420 Å2
ΔGint-114 kcal/mol
Surface area91360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.172, 133.943, 208.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22C
32D
13A
23B
14C
24D
15A
25B
35C
45D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPHEPHEAA40 - 34359 - 362
21PROPROPHEPHEBB40 - 34359 - 362
31PROPROPHEPHECC40 - 34359 - 362
41PROPROPHEPHEDD40 - 34359 - 362
12ARGARGLYSLYSAA4 - 2923 - 48
22ARGARGLYSLYSCC4 - 2923 - 48
32ARGARGLYSLYSDD4 - 2923 - 48
13GLUGLUUNKUNKAA345 - 1537364 - 607
23GLUGLUUNKUNKBB345 - 1537364 - 604
14GLUGLUUNKUNKCC345 - 1537364 - 646
24GLUGLUUNKUNKDD345 - 1537364 - 647
15UNKUNKUNKUNKAA2214 - 2276615 - 665
25UNKUNKUNKUNKBB2215 - 2275612 - 648
35UNKUNKUNKUNKCC2210 - 2275647 - 701
45UNKUNKUNKUNKDD2216 - 2276648 - 685

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein phosphoseryl-tRNA synthetase / O-phospho-L-serine—tRNA ligase


Mass: 72592.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: S2 / Gene: MMP0688 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 codon plus (DE3) RIL
References: UniProt: Q6LZE1, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds
#2: Protein phosphoseryl-tRNA synthetase / O-phospho-L-serine—tRNA ligase


Mass: 71146.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: S2 / Gene: MMP0688 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 codon plus (DE3) RIL
References: UniProt: Q6LZE1, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds
#3: Protein phosphoseryl-tRNA synthetase / O-phospho-L-serine—tRNA ligase


Mass: 75656.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: S2 / Gene: MMP0688 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 codon plus (DE3) RIL
References: UniProt: Q6LZE1, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds
#4: Protein phosphoseryl-tRNA synthetase / O-phospho-L-serine—tRNA ligase


Mass: 74339.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: S2 / Gene: MMP0688 / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 codon plus (DE3) RIL
References: UniProt: Q6LZE1, Ligases; Forming carbon-oxygen bonds; Ligases forming aminoacyl-tRNA and related compounds

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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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Well:4-6% PEG 35,000, 5 mM DTT, 100 mM Sodium MES (pH 6.5), 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211.0039
SYNCHROTRONALS 8.2.221.214
SYNCHROTRONALS 8.2.231.0716
Detector
TypeIDDetector
ADSC QUANTUM 2101CCD
ADSC QUANTUM 3152CCD
ADSC QUANTUM 2103CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
3Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.00391
21.2141
31.07161
Reflection

D res low: 50 Å

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)Num. obs% possible obs
3.817.51576980.0871.054.441750100
3.227.91201200.081.014.53710895.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
9.465099.810.0411.0513.7
7.529.4610010.0521.0313.8
6.577.5210010.1020.9753.8
5.976.5710010.1791.0293.8
5.545.9710010.2681.0533.8
5.225.5410010.331.0533.8
4.965.2210010.4091.0693.8
4.744.9610010.461.0763.8
4.564.7410010.5571.0753.7
4.44.5610010.8491.0923.7
9.675099.920.0330.9373.8
7.699.6710020.0470.9353.8
6.727.6910020.1271.0293.8
6.116.7210020.2321.063.8
5.676.1110020.3821.0593.8
5.335.6799.820.4781.0173.5
5.075.339820.5141.0182.9
4.855.0793.720.5521.0572.4
4.664.8585.420.6031.0522.1
4.54.667420.8380.9921.9
ReflectionResolution: 3.2→50 Å / Num. all: 53862 / Num. obs: 53215 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.053 / Χ2: 1.035 / Net I/σ(I): 11
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.907 / Mean I/σ(I) obs: 1.1 / Num. unique all: 4992 / Χ2: 1.036 / % possible all: 94.4

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Phasing

PhasingMethod: MIR
Phasing MIRResolution: 4.5→50 Å / FOM: 0.52 / Reflection: 19624
Phasing MIR der
IDDer set-ID
11
21
31
41
Phasing MIR der site

Biso : 60 Å

IDDer-IDAtom type symbolFract xFract yFract zOccupancy
11W0.09720.13530.24671.0772
12W0.8090.94170.13060.9662
13W0.03020.20710.11390.7101
14W0.25840.54680.25160.6198
21Sm0.33810.62710.24080.8075
22Sm0.8240.55410.23380.7172
23Sm0.86340.84740.12380.7872
24Sm0.9770.29580.09990.7684
Phasing MIR shell
Resolution (Å)FOMReflection
15.87-500.61973
10.13-15.870.631683
7.95-10.130.632133
6.76-7.950.632464
5.98-6.760.582744
5.41-5.980.52971
4.99-5.410.423230
4.64-4.990.343426

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 3.228→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.893 / SU B: 55.877 / SU ML: 0.461 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2697 5.1 %RANDOM
Rwork0.292 ---
obs0.292 53170 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 115.697 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å20 Å20 Å2
2---1.63 Å20 Å2
3---3.15 Å2
Refinement stepCycle: LAST / Resolution: 3.228→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13538 0 0 0 13538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02213726
X-RAY DIFFRACTIONr_bond_other_d0.0010.028914
X-RAY DIFFRACTIONr_angle_refined_deg1.041.95118541
X-RAY DIFFRACTIONr_angle_other_deg0.842321778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02351795
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03124.423520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.539152118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6161557
X-RAY DIFFRACTIONr_chiral_restr0.0620.22158
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022699
X-RAY DIFFRACTIONr_nbd_refined0.2240.23396
X-RAY DIFFRACTIONr_nbd_other0.1840.29440
X-RAY DIFFRACTIONr_nbtor_refined0.1820.26675
X-RAY DIFFRACTIONr_nbtor_other0.0860.27699
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5880.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.5210.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.22
X-RAY DIFFRACTIONr_mcbond_it0.3781.511705
X-RAY DIFFRACTIONr_mcbond_other0.1461.53722
X-RAY DIFFRACTIONr_mcangle_it0.498214346
X-RAY DIFFRACTIONr_scbond_it0.73235418
X-RAY DIFFRACTIONr_scangle_it0.9764.54195
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3237TIGHT POSITIONAL0.020.05
12B3237TIGHT POSITIONAL0.020.05
13C3237TIGHT POSITIONAL0.020.05
14D3237TIGHT POSITIONAL0.020.05
11A3237TIGHT THERMAL0.040.5
12B3237TIGHT THERMAL0.040.5
13C3237TIGHT THERMAL0.040.5
14D3237TIGHT THERMAL0.040.5
21A370TIGHT POSITIONAL0.010.05
22C370TIGHT POSITIONAL0.010.05
23D370TIGHT POSITIONAL0.010.05
21A370TIGHT THERMAL0.020.5
22C370TIGHT THERMAL0.020.5
23D370TIGHT THERMAL0.020.5
31A1808TIGHT POSITIONAL0.020.05
31A1808TIGHT THERMAL0.020.5
41C1249TIGHT POSITIONAL0.020.05
41C1249TIGHT THERMAL0.030.5
51A238TIGHT POSITIONAL0.010.05
52B238TIGHT POSITIONAL0.010.05
53C238TIGHT POSITIONAL0.010.05
54D238TIGHT POSITIONAL0.010.05
51A238TIGHT THERMAL0.020.5
52B238TIGHT THERMAL0.020.5
53C238TIGHT THERMAL0.020.5
54D238TIGHT THERMAL0.010.5
LS refinement shellResolution: 3.228→3.312 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 178 -
Rwork0.373 3037 -
obs-3215 80.74 %
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)
11.47620.68640.26442.4430.31093.95540.20230.174-0.0620.61870.0146-0.54030.2220.7124-0.2169-0.53460.1664-0.0652-0.6608-0.0713-0.117269.518916.448747.2078
22.39660.4654-0.20151.77850.58364.6419-0.06940.71920.4001-0.030.2152-0.0258-0.49950.2752-0.1458-0.50560.02860.0064-0.70980.128-0.120862.050226.757728.9038
31.71950.47050.75991.99780.55774.33650.161-0.15480.03640.5997-0.0580.867-0.0606-0.998-0.103-0.51260.13990.1277-0.41420.11750.136630.60397.073347.2555
42.13370.2959-0.23231.66660.46045.21880.07290.5357-0.54870.15150.11350.45290.8621-0.3275-0.1864-0.39620.0178-0.1313-0.68190.06650.015438.7769-5.86831.5113
54.4108-3.64041.889811.0452-2.98186.5553-0.47010.3925-0.31510.19930.20860.67310.8446-1.62270.26150.3024-0.1378-0.3640.48-0.06830.379327.3216-12.51837.0484
68.525-3.9841-2.92382.859-2.03712.61970.00610.78360.2784-0.82730.59-0.7543-0.6890.9744-0.5962-0.0384-0.26540.20920.34570.10490.209973.976929.2834.3168
712.2256-0.8233-1.73852.1122.318212.04330.1014-1.40730.47841.5862-0.0908-0.7872-0.04420.3211-0.01060.272-0.0905-0.278-0.2818-0.201-0.018877.906727.653371.1288
84.65630.46861.53532.95041.90184.2857-0.14110.4324-0.2892-0.03550.4504-0.3352-0.36520.3628-0.3093-0.18950.0311-0.06-0.0543-0.1206-0.009861.1015-12.48681.5342
93.17581.4118-3.44713.1965-1.83245.4610.3989-0.28170.35440.1037-0.08350.0949-0.16290.4993-0.3153-0.11350.05960.145-0.2131-0.09760.081633.694232.126474.9978
105.02350.2188-0.33441.1521-1.68292.4583-0.01641.09450.6948-1.16430.1799-0.003-0.56560.6044-0.16350.287-0.1435-0.16640.62140.32610.256443.94527.9817-9.6182
111.2911.38130.05621.6246-0.11753.9193-0.0335-1.1038-0.11830.75960.0729-0.0560.1140.5011-0.03940.6266-0.0486-0.24070.2132-0.03650.082964.82881.333987.6441
120.12831.3412-0.850414.0238-8.89155.63750.51830.4607-0.393-1.2462-0.18310.1234-0.6606-0.0979-0.33520.3534-0.04030.31530.4707-0.10510.2479.013252.139615.5701
1322.93616.0935.27625.16415.863826.6165-0.6687-0.85470.22490.2897-0.3890.4921-0.5094-0.37371.05770.29190.2108-0.21620.3728-0.10840.657599.740122.380856.707
140.5349-0.9104-2.19077.42192.779.12810.75820.9705-0.4101-1.1698-0.3322-0.06990.9145-0.2385-0.42610.1875-0.1593-0.36470.5011-0.02590.520122.6117-33.310523.026
1519.66256.8656-8.80426.7201-5.756730.31590.1228-0.19890.02041.0339-0.76120.1857-0.28520.48010.63840.28530.10760.1260.48840.05980.76210.82470.629658.6197
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA30 - 34349 - 362
22BB31 - 34350 - 362
33CC30 - 34349 - 362
44DD30 - 34349 - 362
55AA4 - 2623 - 45
66CC4 - 2623 - 45
77DD4 - 2623 - 45
88AA345 - 1997364 - 614
99BB345 - 1997364 - 611
1010CC1364 - 1537557 - 646
1111DD1364 - 1537557 - 647
1212AA2214 - 2276615 - 665
1313BB2215 - 2275612 - 648
1414CC2210 - 2275647 - 701
1515DD2216 - 2276648 - 685

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