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- PDB-6oiy: Structure of Escherichia coli bound to dGTP -

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Basic information

Entry
Database: PDB / ID: 6oiy
TitleStructure of Escherichia coli bound to dGTP
ComponentsDeoxyguanosinetriphosphate triphosphohydrolase
Keywordsmetal binding protein / hydrolase / dNTP Triphosphohydrolase / Metalloenzymes / E. coli dGTPase
Function / homology
Function and homology information


dGTPase / dGTPase activity / dGTP catabolic process / nucleobase-containing small molecule interconversion / cobalt ion binding / single-stranded DNA binding / manganese ion binding / GTPase activity / magnesium ion binding / identical protein binding
Similarity search - Function
Phosphohydrolase-associated domain / dNTP triphosphohydrolase, type 1 / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. ...Phosphohydrolase-associated domain / dNTP triphosphohydrolase, type 1 / Deoxyguanosinetriphosphate triphosphohydrolase, central domain superfamily / dNTP triphosphohydrolase / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / Deoxyguanosinetriphosphate triphosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsBarnes, C.O. / Wu, Y. / Calero, G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112686 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM116642 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity.
Authors: Barnes, C.O. / Wu, Y. / Song, J. / Lin, G. / Baxter, E.L. / Brewster, A.S. / Nagarajan, V. / Holmes, A. / Soltis, S.M. / Sauter, N.K. / Ahn, J. / Cohen, A.E. / Calero, G.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyguanosinetriphosphate triphosphohydrolase
B: Deoxyguanosinetriphosphate triphosphohydrolase
C: Deoxyguanosinetriphosphate triphosphohydrolase
D: Deoxyguanosinetriphosphate triphosphohydrolase
E: Deoxyguanosinetriphosphate triphosphohydrolase
F: Deoxyguanosinetriphosphate triphosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)360,19818
Polymers356,8256
Non-polymers3,37312
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26850 Å2
ΔGint-91 kcal/mol
Surface area105590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.176, 192.176, 299.596
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Deoxyguanosinetriphosphate triphosphohydrolase / dGTPase


Mass: 59470.863 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dgt, b0160, JW0156 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15723, dGTPase
#2: Chemical
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.88 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCl pH 8.0 and 1.6 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.29→48 Å / Num. obs: 85237 / % possible obs: 99 % / Redundancy: 7.1 % / Biso Wilson estimate: 115 Å2 / Rmerge(I) obs: 0.252 / Net I/σ(I): 7.1
Reflection shellResolution: 3.29→3.38 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5772 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→46.87 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.37
RfactorNum. reflection% reflection
Rfree0.241 1970 2.35 %
Rwork0.205 --
obs0.206 83729 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.29→46.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24513 0 192 12 24717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01325316
X-RAY DIFFRACTIONf_angle_d1.39934278
X-RAY DIFFRACTIONf_dihedral_angle_d16.44915121
X-RAY DIFFRACTIONf_chiral_restr0.0673644
X-RAY DIFFRACTIONf_plane_restr0.0094387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2939-3.37620.33791130.33644571X-RAY DIFFRACTION78
3.3762-3.46750.36051390.32225772X-RAY DIFFRACTION99
3.4675-3.56950.30961410.31175871X-RAY DIFFRACTION100
3.5695-3.68470.33161410.30595853X-RAY DIFFRACTION100
3.6847-3.81630.31751410.26775862X-RAY DIFFRACTION100
3.8163-3.9690.27411420.24415882X-RAY DIFFRACTION100
3.969-4.14960.26171410.23825889X-RAY DIFFRACTION100
4.1496-4.36820.24151430.21365915X-RAY DIFFRACTION100
4.3682-4.64160.23051420.18295923X-RAY DIFFRACTION100
4.6416-4.99970.21241440.18435929X-RAY DIFFRACTION100
4.9997-5.50210.24631440.19995971X-RAY DIFFRACTION100
5.5021-6.29660.26541430.21785981X-RAY DIFFRACTION100
6.2966-7.92690.31221460.21486071X-RAY DIFFRACTION100
7.9269-46.87340.18361500.16696269X-RAY DIFFRACTION99
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)
12.17082.22320.11663.3619-0.1651.3619-0.02370.27050.0099-0.05720.0104-0.07010.21070.17630.00021.18060.0556-0.01081.46440.04251.330459.489136.825222.3078
20.97380.0143-0.49192.22580.66691.29480.4517-0.5935-0.48690.84520.875-1.7990.48650.57910.08171.5001-0.2107-0.34132.51590.1321.361287.168947.539239.5066
32.88952.07360.2881.29170.00441.26720.1409-0.481-0.12340.1056-0.1932-0.21170.19150.3545-0.00011.17890.04850.03891.28520.11851.385854.380230.99231.062
4-0.10740.87141.68340.03710.59992.66310.1857-0.4195-0.31260.104-0.1534-0.17050.62940.0825-0.45251.67220.2012-0.1562.13840.21061.691473.88871.914171.8279
51.69651.48690.31828.09971.00491.6899-0.6085-0.34040.380.9902-0.07231.59460.1883-0.6578-0.96841.0836-0.13560.09941.75690.04761.106250.599211.022694.7178
61.1903-1.01010.43372.29880.90021.56760.2291-0.2501-0.21780.3633-0.2575-0.16180.1352-0.3185-0.00051.58470.0903-0.12341.80850.19651.604365.11438.320165.3965
71.40170.28862.30071.57730.03471.89350.9116-0.3642-0.4160.786-0.47920.55030.13690.1840.09861.19550.12440.21091.38970.16861.439110.285318.675669.1914
80.7806-0.08560.6172-0.23150.50861.36750.3817-0.8324-0.33060.6558-0.20150.0042-0.2693-0.3516-0.00091.2389-0.05740.07321.35370.33341.67940.146624.750463.5228
90.8907-3.1492-1.48152.23721.05161.68240.13820.1725-0.1838-0.4384-0.12160.01920.1957-0.4538-0.00021.23230.00590.02951.13750.04481.32417.82348.312652.9143
103.06764.82773.8319.01546.58014.66960.4078-0.78132.4316-0.7683-0.96951.6414-1.1148-1.1416-1.69891.42450.05820.12141.25780.17281.524210.999745.33943.8392
111.4908-0.1031-1.19310.6788-0.48360.53430.3381-0.10540.3625-0.6636-0.4037-0.1192-0.23810.355301.405-0.03270.1431.55910.01761.77265.436130.263748.5082
124.4806-0.38970.41931.42490.07932.62050.5502-0.6179-0.84460.1443-0.1856-0.1349-0.0031-0.12630.00041.29010.00310.01871.6160.1371.690935.53467.393461.2368
13-0.00530.0937-0.18420.28980.14290.28311.1878-0.60220.5280.3534-1.12280.43172.99791.1368-0.00042.6112-0.2078-0.23343.08910.07991.725877.317220.0629103.6449
140.10890.4277-0.06321.1967-0.0756-0.0027-0.66640.251.04920.22450.1631-0.7976-0.99690.95480.00071.9753-0.1446-0.22422.6860.35372.121775.139425.910380.3496
15-0.0014-0.14560.13690.0283-0.10970.2494-1.68391.33011.1484-0.59940.7837-0.55841.07171.1736-0.01322.1569-0.3118-0.82862.82950.27652.156688.294321.060996.3309
16-0.4298-0.02140.1871.3223-1.54291.63130.21930.3080.4889-0.4015-0.54871.00830.92010.554801.8757-0.3093-0.10782.0547-0.1561.713663.490854.083293.145
170.294-0.22710.64431.47490.20720.50240.45-0.040.44680.35190.203-0.82980.14030.55601.9134-0.2019-0.24212.56640.13071.980879.892936.279885.6745
181.6415-0.328-0.60850.822-0.29570.314-0.635-0.35870.28110.61770.0434-0.1219-0.32830.69450.00141.83210.0339-0.4842.61860.00292.098189.952533.336878.7389
190.4497-0.5360.5380.4409-0.55710.5517-0.40450.4144-0.2126-0.99610.0302-0.1262-0.08850.97080.00061.823-0.0865-0.02611.735-0.07991.649158.381845.774377.1788
200.33260.2073-0.10880.37160.08150.0576-0.1303-1.084-0.77910.55720.7203-0.1833-0.5240.9784-0.00021.8919-0.1388-0.10692.5646-0.03241.423447.030141.921197.9576
210.7268-0.62280.20420.2719-0.13720.19790.3822-0.5217-0.03320.5469-0.0541-0.17490.4417-0.1313-0.00011.7118-0.1628-0.07852.28520.14541.628255.015841.413886.4861
220.9268-0.32210.38330.00790.12740.75350.62671.01280.2062-0.14160.16050.2431-0.5538-1.73520.00171.49790.2640.32091.62450.26671.9206-2.534844.237369.8748
230.5216-0.0174-1.19191.3591.70283.46660.0584-0.3885-0.49820.6958-0.1949-0.37250.0860.5765-0.00011.34630.01490.04731.46380.12831.47910.156533.286276.4112
240.92111.64780.452.26241.32761.69770.3052-0.09110.17130.21250.2056-0.3335-0.160.334201.2266-0.15820.20671.2789-0.20361.549519.005356.653482.1548
251.53991.29820.9391.2736-0.38061.18510.3428-0.29060.06740.8698-0.5943-0.49590.15510.3365-0.00011.6844-0.07370.07751.9860.22751.792718.494626.011489.8686
261.28080.21190.20330.148-0.10020.00120.5166-0.184-0.93450.7066-0.2282-0.57880.24490.96730.0021.4955-0.3403-0.07781.85380.24882.021738.400448.204575.4554
270.5991-0.45380.84360.0561-0.16781.223-0.0152-0.46381.4609-0.03670.3333-0.39440.13050.2220.00071.5997-0.13990.12641.8119-0.09482.329327.675565.390762.4868
280.0168-0.30080.19490.7034-0.57630.27770.46760.75480.313-0.7039-0.0581-0.91440.2829-0.28910.00021.4603-0.21470.24571.6437-0.08091.628531.322353.716869.0826
290.6860.1449-0.67610.5232-0.10120.5168-0.7484-0.28520.135-0.25430.08-0.83060.25170.2328-0.00021.4263-0.0617-0.00661.5554-0.01931.728673.314968.304129.2928
300.7023-0.8623-0.34971.4282-0.1770.53040.2184-0.3742-0.52240.73730.25420.9483-0.946-0.65980.00011.2809-0.07390.0481.49220.08241.430153.823357.171634.6481
310.03110.09520.10170.54820.48220.35560.92960.0079-0.2178-0.4959-0.47720.2615-0.44081.06180.00051.43420.18050.03781.49160.11061.57462.65869.884423.7127
32-0.0755-0.1278-0.26970.24410.63070.3204-0.0053-0.7997-0.05040.6336-0.39720.35090.0225-0.69440.00021.8889-0.37410.01982.1598-0.33561.642557.568673.827663.5801
331.01980.7353-0.53870.90190.21981.57080.2821-0.56750.76650.685-0.2696-0.3849-1.0542-0.01620.00031.68610.05360.10881.4692-0.02291.606461.997374.419745.0059
340.6273-0.1525-0.25690.68940.4080.4973-0.3083-0.32510.6375-0.1982-0.6530.9407-0.4262-0.575-0.00071.413-0.3213-0.14972.16470.1171.932335.969158.506232.2295
350.2140.0651-0.09190.0380.03430.560.81480.17330.4608-0.6414-0.56980.64220.07160.481801.4958-0.0493-0.07411.84780.16432.11342.522462.489125.221
360.46630.22130.5628-0.11890.03090.59160.2254-1.11240.35921.0353-0.09020.5729-1.4656-0.4138-0.00061.82290.15220.09591.80160.09121.958542.578371.195335.6267
370.49530.0021-0.5845-0.01350.11450.56740.50.5662-1.0510.6394-0.35980.5366-0.4737-0.435-0.00211.4715-0.43580.0032.4287-0.08461.425750.924456.30661.9446
380.96770.8038-0.65960.7302-0.70070.4060.5745-0.6519-0.2050.6444-0.7398-0.7151-0.49430.1946-0.00081.7191-0.3708-0.05852.0133-0.01641.627468.529959.673763.5933
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 298 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 299 THROUGH 329 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 330 THROUGH 504 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 2 THROUGH 271 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 272 THROUGH 328 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 329 THROUGH 504 )
7X-RAY DIFFRACTION7CHAIN 'C' AND (RESID 2 THROUGH 65 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 66 THROUGH 116 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 117 THROUGH 282 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 283 THROUGH 327 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 328 THROUGH 393 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 394 THROUGH 504 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 3 THROUGH 40 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 41 THROUGH 87 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 88 THROUGH 116 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 117 THROUGH 180 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 181 THROUGH 327 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 328 THROUGH 393 )
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 394 THROUGH 419 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 420 THROUGH 468 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 469 THROUGH 504 )
22X-RAY DIFFRACTION22CHAIN 'E' AND (RESID 3 THROUGH 40 )
23X-RAY DIFFRACTION23CHAIN 'E' AND (RESID 41 THROUGH 116 )
24X-RAY DIFFRACTION24CHAIN 'E' AND (RESID 117 THROUGH 260 )
25X-RAY DIFFRACTION25CHAIN 'E' AND (RESID 261 THROUGH 393 )
26X-RAY DIFFRACTION26CHAIN 'E' AND (RESID 394 THROUGH 419 )
27X-RAY DIFFRACTION27CHAIN 'E' AND (RESID 420 THROUGH 468 )
28X-RAY DIFFRACTION28CHAIN 'E' AND (RESID 469 THROUGH 504 )
29X-RAY DIFFRACTION29CHAIN 'F' AND (RESID 3 THROUGH 40 )
30X-RAY DIFFRACTION30CHAIN 'F' AND (RESID 41 THROUGH 90 )
31X-RAY DIFFRACTION31CHAIN 'F' AND (RESID 91 THROUGH 116 )
32X-RAY DIFFRACTION32CHAIN 'F' AND (RESID 117 THROUGH 180 )
33X-RAY DIFFRACTION33CHAIN 'F' AND (RESID 181 THROUGH 260 )
34X-RAY DIFFRACTION34CHAIN 'F' AND (RESID 261 THROUGH 327 )
35X-RAY DIFFRACTION35CHAIN 'F' AND (RESID 328 THROUGH 354 )
36X-RAY DIFFRACTION36CHAIN 'F' AND (RESID 355 THROUGH 393 )
37X-RAY DIFFRACTION37CHAIN 'F' AND (RESID 394 THROUGH 419 )
38X-RAY DIFFRACTION38CHAIN 'F' AND (RESID 420 THROUGH 504 )

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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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