[English] 日本語
Yorodumi
- PDB-6nqk: Crystal structure of fast switching M159T mutant of fluorescent p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6nqk
TitleCrystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2), Y63(3-FY)
ComponentsFluorescent protein DronpaFluorescence
KeywordsFLUORESCENT PROTEIN / Dronpa2
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fluorescent protein Dronpa
Similarity search - Component
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, C.-Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)27738 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118044 United States
CitationJournal: Science / Year: 2020
Title: Electrostatic control of photoisomerization pathways in proteins.
Authors: Romei, M.G. / Lin, C.Y. / Mathews, I.I. / Boxer, S.G.
History
DepositionJan 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.5Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fluorescent protein Dronpa
B: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa
G: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)231,8378
Polymers231,8378
Non-polymers00
Water25,1671397
1
A: Fluorescent protein Dronpa

G: Fluorescent protein Dronpa

C: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,9184
Polymers115,9184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
2
F: Fluorescent protein Dronpa

D: Fluorescent protein Dronpa

B: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,9184
Polymers115,9184
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Unit cell
Length a, b, c (Å)81.750, 86.480, 143.810
Angle α, β, γ (deg.)90.00, 94.89, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Fluorescent protein Dronpa / Fluorescence


Mass: 28979.568 Da / Num. of mol.: 8 / Mutation: M159T, E218G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echinophyllia sp. SC22 (invertebrata) / Gene: Dronpa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5TLG6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1397 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M Tris-HCl at pH 7.4, 0.1 M MgCl2, 12% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.195 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.195 Å / Relative weight: 1
ReflectionResolution: 2→39.756 Å / Num. obs: 134566 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 34.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.092 / Net I/σ(I): 14.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.2 % / Num. unique obs: 9849 / CC1/2: 0.81 / Rrim(I) all: 0.86 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(1.13RC2_2986: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTS
Resolution: 2→39.756 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.72
RfactorNum. reflection% reflection
Rfree0.222 6714 5 %
Rwork0.195 --
obs0.196 134335 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13917 0 0 1397 15314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514783
X-RAY DIFFRACTIONf_angle_d0.97819991
X-RAY DIFFRACTIONf_dihedral_angle_d5.21111942
X-RAY DIFFRACTIONf_chiral_restr0.0572009
X-RAY DIFFRACTIONf_plane_restr0.0062604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9999-2.02270.32452190.29744173X-RAY DIFFRACTION98
2.0227-2.04640.32132250.27794268X-RAY DIFFRACTION99
2.0464-2.07140.31132190.27054156X-RAY DIFFRACTION100
2.0714-2.09760.2832250.25914284X-RAY DIFFRACTION100
2.0976-2.12520.28032230.24454230X-RAY DIFFRACTION100
2.1252-2.15430.2952240.24574266X-RAY DIFFRACTION100
2.1543-2.18510.28282210.24074181X-RAY DIFFRACTION100
2.1851-2.21770.2712250.24154275X-RAY DIFFRACTION100
2.2177-2.25240.30042240.2374247X-RAY DIFFRACTION100
2.2524-2.28930.29772240.23064262X-RAY DIFFRACTION100
2.2893-2.32880.26872250.22914268X-RAY DIFFRACTION100
2.3288-2.37110.2582220.23184218X-RAY DIFFRACTION100
2.3711-2.41670.26592250.234260X-RAY DIFFRACTION100
2.4167-2.4660.26292230.22584237X-RAY DIFFRACTION100
2.466-2.51960.24072250.21634267X-RAY DIFFRACTION100
2.5196-2.57820.25042230.20834250X-RAY DIFFRACTION100
2.5782-2.64270.24852260.20334274X-RAY DIFFRACTION100
2.6427-2.71410.25062230.21024273X-RAY DIFFRACTION100
2.7141-2.7940.23542220.2014222X-RAY DIFFRACTION99
2.794-2.88420.28482240.21554253X-RAY DIFFRACTION100
2.8842-2.98720.23542240.22214252X-RAY DIFFRACTION100
2.9872-3.10680.24352240.2194253X-RAY DIFFRACTION100
3.1068-3.24810.23192240.20314263X-RAY DIFFRACTION100
3.2481-3.41930.22552260.1934307X-RAY DIFFRACTION100
3.4193-3.63330.22052230.18524235X-RAY DIFFRACTION100
3.6333-3.91370.18042250.1724282X-RAY DIFFRACTION100
3.9137-4.30710.16722240.1524278X-RAY DIFFRACTION100
4.3071-4.92930.16242220.13964254X-RAY DIFFRACTION99
4.9293-6.20660.17412270.15544313X-RAY DIFFRACTION99
6.2066-39.7560.18962280.19034320X-RAY DIFFRACTION98
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)
12.59032.0807-0.09912.1276-1.27472.36530.7694-1.213-0.24470.5171-1.0053-0.1241-0.00750.07420.15580.3712-0.04020.07430.4373-0.02630.42445.25621.598526.4716
26.91035.09341.99394.00211.83752.32510.1945-0.22310.1130.2631-0.1650.1707-0.1658-0.29790.09740.4092-0.05070.08240.3228-0.03550.30666.01258.632227.0161
37.05664.83531.97586.02432.6852.74750.2912-0.951-0.20220.1768-0.40140.1752-0.0317-0.69890.14350.352-0.0440.06690.5442-0.00840.3395-1.33563.005224.0996
41.40160.32450.08472.16290.30230.89370.1178-0.2783-0.01930.292-0.26110.0470.1022-0.18230.11960.3007-0.04440.04630.3626-0.0360.26738.35553.281517.9516
52.1204-4.5633-0.44649.68610.62690.1130.103-0.00460.0057-0.0041-0.12080.16830.0406-0.0650.04030.2533-0.02030.02140.3179-0.02910.34517.56582.25117.5297
61.34450.0034-0.28462.4301-0.17811.05390.0856-0.0777-0.1036-0.0973-0.0980.24090.0278-0.29170.01150.2553-0.02550.01980.3347-0.03140.31865.89470.777710.9011
72.2042-0.3587-2.05472.64842.29635.63410.1815-0.01230.14620.0123-0.41340.3702-0.0634-1.07740.54420.24450.0114-0.00740.4295-0.02710.4476-2.41074.270514.0574
87.7015-5.8083-0.83216.51362.29881.81420.20690.09680.0597-0.3161-0.0588-0.12630.0180.1868-0.20380.40030.01830.10930.38850.08920.3042-11.4978-39.264745.0295
92.9762-0.9042.92723.7533-4.59586.7110.06970.61030.6285-0.1774-0.4424-0.88950.21040.5970.30720.32530.01490.04370.3091-0.00070.256-8.2535-37.34746.9745
102.6195-2.38031.13475.2286-2.08662.41430.06440.29180.2822-0.2662-0.4265-0.4445-0.1570.16670.36360.2898-0.03230.06080.31790.06670.3773-10.5582-29.305648.3223
111.84592.1342-0.93473.634-3.60176.21430.0739-0.0555-0.2301-0.2215-0.06240.11070.23470.2165-0.02550.32510.0580.07020.27510.02270.2625-7.802-46.169557.211
121.4843-0.54810.00472.8423-0.3922-0.0047-0.03430.1607-0.19830.0753-0.17730.25360.30420.04510.18180.33540.03250.0110.28770.01440.1966-17.2257-42.53755.7203
131.5339-1.208-0.40375.15121.35042.28010.130.2060.1883-0.433-0.1664-0.2250.04010.18110.05690.30640.01540.01280.3340.07260.2931-17.3133-32.576751.1463
142.6162.6575-1.01428.777-0.62050.5477-0.00740.0976-0.10.036-0.0219-0.18020.05630.15880.08010.2523-0.01080.00610.29640.04510.2494-13.7887-38.274664.0953
153.48691.70712.41684.95453.97954.56170.2678-0.0910.24580.33-0.4714-0.3488-0.2395-0.1610.14160.3460.00230.03160.29030.0390.296-15.6778-33.17962.8503
160.7307-0.4588-0.97173.5214-0.93151.76360.1068-0.05710.028-0.0118-0.2962-0.20640.09220.29090.13770.26210.06230.00720.33270.08110.4212-9.7301-44.451759.1589
171.641-0.1152-0.43725.4338-3.38185.7016-0.06950.02960.1107-0.01210.0823-0.2373-0.06510.30290.33270.1833-0.01140.05090.35730.0170.4439-3.7973-36.363757.6488
188.3831-1.7999-0.75282.1693-0.25741.9949-0.4146-0.4954-1.11290.18180.2150.1194-0.0387-0.24890.1920.3589-0.03860.00490.3033-0.02940.2399-35.4516-27.702624.194
193.31940.98981.80462.15841.02122.25550.0132-0.18020.18210.1231-0.18970.0365-0.0527-0.21310.1890.3196-0.01910.03720.304-0.04060.2401-32.846-23.354120.1365
200.3479-0.7496-0.34116.8377-0.70637.09190.0332-0.2363-0.15050.13680.00650.6849-0.0836-0.5336-0.01540.233-0.05390.03350.3924-0.00160.3786-47.6923-35.4413.5254
213.07151.0451-0.93321.5609-0.98710.8401-0.0013-0.2289-0.00320.1184-0.01480.0314-0.0151-0.03610.05030.3266-0.01650.01340.28320.0080.2541-30.454-32.433817.6019
224.3606-5.4271-1.72296.73782.05855.7835-0.00510.21610.41930.1106-0.2532-0.63-0.13710.13220.17730.2891-0.0478-0.010.29210.01830.3751-15.8097-19.072510.8367
234.48343.06151.16542.42171.10762.07270.0020.0772-0.2946-0.27240.0998-0.4151-0.1531-0.0385-0.07730.2195-0.00670.01370.23470.01250.239-33.439-29.46775.0995
242.71242.1542-1.85883.0225-3.04183.5244-0.2688-0.0928-0.0338-0.28230.0578-0.33080.010.05660.23290.2338-0.01210.02310.207-0.0490.2448-28.5448-27.50026.4811
251.74990.84250.95622.15081.12153.7587-0.0670.0692-0.0208-0.16950.07010.2092-0.1227-0.2707-0.0140.19880.00010.0340.30590.01550.2857-40.7147-30.382410.1911
262.18371.20080.35243.45812.56953.7388-0.0365-0.27730.73510.0818-0.49270.599-0.1133-0.65590.70710.33920.0948-0.05110.24930.02190.3155-38.6953-20.629311.6542
271.78120.6362-1.61031.4790.44992.3735-0.2070.3225-0.5852-0.29130.0894-0.06730.1830.09650.02030.51350.03760.02760.33540.0540.3034-52.502818.198247.4353
283.9861-1.00641.23342.3855-0.44011.8333-0.13680.30820.1409-0.1733-0.00030.0529-0.25960.15320.16440.406-0.03270.00390.29090.03340.2394-55.554522.939151.3527
290.41860.14170.68185.0570.25759.2038-0.11310.0624-0.1328-0.0773-0.0303-0.36460.30060.51310.06220.22370.02530.06940.32860.05080.2948-40.244611.086858.0155
302.096-0.5722-0.53910.96570.8310.63790.01620.27160.0453-0.1809-0.02660.0173-0.19890.10290.00760.3905-0.0187-0.00550.29690.01960.251-57.50913.845754.0073
316.18815.1712-0.414.3337-0.58992.747-0.0344-0.16840.4817-0.17850.11570.7991-0.0377-0.1060.01130.320.0646-0.06540.31540.0210.4091-72.261626.97260.8068
324.5336-4.84711.03719.3516-0.74971.6331-0.1093-0.006-0.26710.46630.14340.1936-0.00810.1510.00120.2689-0.02490.04070.259-0.00350.2353-54.481117.260666.2911
333.5869-2.6914-2.03594.50823.86353.6274-0.11940.0064-0.01090.1351-0.11210.14840.0046-0.00630.26780.27230.01870.00450.22870.01320.2097-59.439918.780765.1113
342.1514-1.38930.56793.0716-1.73911.9625-0.11910.07380.2074-0.01110.0406-0.1598-0.29190.19460.08070.3319-0.0389-0.00650.30860.00340.3127-48.484720.575160.7062
355.7491-2.0811-0.37853.43070.11623.2977-0.283-0.88790.2350.26180.1182-0.26660.08770.31430.13440.3654-0.0099-0.0450.26240.02470.2579-6.8804-43.279524.4173
364.01590.661-1.14072.0875-0.44112.2579-0.2318-0.2325-0.007-0.0347-0.0227-0.2880.26570.22970.21210.28880.0048-0.04390.28560.04550.3134-7.5529-46.818818.7762
370.0401-0.4628-0.38433.1414-0.45684.4915-0.0933-0.17250.00850.0315-0.0022-0.4193-0.160.3330.0760.2488-0.0701-0.05560.46590.02540.43077.1169-34.552113.3273
382.95640.80041.00672.09860.88141.0537-0.0705-0.2194-0.1320.1869-0.00450.00190.0065-0.02810.07410.2459-0.0048-0.00780.23590.03710.2555-10.5997-37.538117.4042
395.291-5.65322.86076.0242-3.19723.20710.14150.534-0.416-0.0378-0.14180.45150.23970.1245-0.00160.271-0.0478-0.00170.2644-0.010.3186-25.1876-51.107510.7514
405.14633.7181-0.87247.7066-1.45041.82680.0284-0.14790.2146-0.5114-0.1635-0.00020.060.24180.12710.25710.0051-0.01940.31350.00140.2619-7.4929-40.49785.1173
413.33752.20262.71435.26514.16873.8136-0.0891-0.1202-0.1321-0.2238-0.007-0.05980.07960.03270.15610.2639-0.01320.00910.29580.03840.2963-12.364-42.44796.5058
422.37660.7572-0.59291.6029-1.0913.7441-0.16330.0416-0.0556-0.05310.1372-0.05550.24230.35470.00360.1990.0197-0.00760.30660.01530.3559-0.169-39.592210.2681
435.49042.3029-2.19623.6743-2.88542.8788-0.2211-0.348-0.306-0.0057-0.1804-0.51480.30690.38820.55110.33820.06310.02910.2308-0.02390.3837-2.8175-48.963811.8418
449.1841.96133.21312.5890.28854.0118-0.56220.38290.835-0.31530.10570.3983-0.1665-0.46230.32660.50360.0031-0.03460.3819-0.08490.3601-0.55633.956247.383
452.6238-0.61630.22791.6293-0.05151.8949-0.06130.2988-0.0267-0.24-0.11790.15470.244-0.18120.17970.3853-0.0472-0.05340.3358-0.05730.28632.0616-0.588551.5395
460.35320.8303-0.75974.8368-0.53637.3528-0.0790.42740.0831-0.03180.09490.5856-0.2117-0.6204-0.05530.28570.0537-0.09040.4441-0.03920.4339-12.921911.31758.1577
473.0939-0.2330.93452.1331-0.97690.6467-0.22470.310.1227-0.1873-0.01930.0219-0.0990.14210.21880.33360.0056-0.0220.2825-0.01840.2494.34778.517354.0688
488.83566.66582.22765.09862.22255.41170.1434-0.142-0.71090.6027-0.0679-0.8420.27790.3572-0.13470.33680.06880.00430.29040.02670.355919.1443-4.66260.8203
494.9317-3.8864-1.01115.79672.02423.0071-0.01910.08850.2370.3866-0.103-0.27880.0413-0.17740.14910.248-0.03-0.02540.22390.02490.20991.39435.465166.5853
503.3433-2.55992.75673.8317-3.45034.4428-0.17710.0694-0.04420.4181-0.0339-0.0024-0.16220.14770.19540.28860.00050.02520.2656-0.02120.2646.28443.589565.1814
511.7829-1.85-1.00842.79231.17332.9152-0.12040.0244-0.19860.25470.07220.41620.0684-0.16260.12260.2113-0.0184-0.01540.2967-0.03730.3816-6.03056.276161.5107
525.9416-3.4728-3.57114.66273.50713.5417-0.29760.3393-0.2369-0.1558-0.12530.50860.2982-0.30640.53250.4398-0.0738-0.02870.27610.00470.3988-3.1945-3.038859.8228
537.09764.18350.94355.39630.66042.79460.4608-0.76140.33550.5389-0.59990.0874-0.08860.10860.19560.3389-0.05420.01360.3831-0.01230.2655-45.85815.647526.5642
545.96614.1796-1.65257.0301-3.4124.0868-0.2879-0.2251-0.4362-0.14150.011-0.64140.12870.26160.20530.3022-0.06290.02340.2725-0.05110.1708-44.270711.88525.0483
550.80040.13160.02181.20730.09530.91390.1059-0.1381-0.02520.2506-0.1758-0.0212-0.03180.11620.08250.3024-0.0340.00240.3240.04330.2763-48.3913.271417.2301
563.7639-3.8951-2.5228.28884.37383.99430.17820.1848-0.1473-0.0913-0.31280.00960.08610.04240.10520.2620.01-0.02270.32190.03450.2383-49.974710.63568.235
571.7807-0.78231.05584.8481-1.59041.76430.0511-0.02180.04990.174-0.124-0.18690.07430.27270.10830.1846-0.0188-0.0020.26420.01110.2194-41.604316.161913.4589
584.7079-3.5142-0.41074.08140.32672.7140.62190.95240.0205-0.7521-0.66960.1991-0.1834-0.13750.03760.34210.0315-0.05270.3774-0.01280.35-42.0942-24.259845.1426
596.4414-5.0957-0.27086.80591.86693.18950.03720.02090.0405-0.4385-0.09740.08250.0178-0.10.05910.4101-0.0440.03930.3018-0.01450.2118-41.0395-32.218744.6564
601.089-0.06-0.1741.21760.26181.43490.00930.15910.0332-0.2077-0.08610.0645-0.09-0.17160.09140.26310.0069-0.02630.2881-0.01190.2228-39.7709-26.653954.4441
612.87112.8643-1.42016.6527-3.76023.81810.19750.0581-0.04230.4245-0.2178-0.0426-0.00050.04840.02840.26560.0139-0.00340.2624-0.02940.2257-37.9816-29.473363.4705
621.91250.04470.61644.04431.7642.24710.0360.0753-0.00290.0787-0.05080.23040.1149-0.32010.00250.26060.0198-0.02110.27650.00260.2744-46.2313-24.191157.9821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 20 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 21 THROUGH 32 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 33 THROUGH 46 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 47 THROUGH 135 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 136 THROUGH 163 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 164 THROUGH 200 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 201 THROUGH 222 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 3 THROUGH 20 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 21 THROUGH 35 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 36 THROUGH 60 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 61 THROUGH 77 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 78 THROUGH 99 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 100 THROUGH 135 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 136 THROUGH 163 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 164 THROUGH 179 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 180 THROUGH 200 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 201 THROUGH 221 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 4 THROUGH 20 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 21 THROUGH 66 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 67 THROUGH 86 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 87 THROUGH 123 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 124 THROUGH 135 )
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 136 THROUGH 163 )
24X-RAY DIFFRACTION24CHAIN 'C' AND (RESID 164 THROUGH 179 )
25X-RAY DIFFRACTION25CHAIN 'C' AND (RESID 180 THROUGH 200 )
26X-RAY DIFFRACTION26CHAIN 'C' AND (RESID 201 THROUGH 221 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 3 THROUGH 20 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 21 THROUGH 66 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 67 THROUGH 86 )
30X-RAY DIFFRACTION30CHAIN 'D' AND (RESID 87 THROUGH 123 )
31X-RAY DIFFRACTION31CHAIN 'D' AND (RESID 124 THROUGH 135 )
32X-RAY DIFFRACTION32CHAIN 'D' AND (RESID 136 THROUGH 163 )
33X-RAY DIFFRACTION33CHAIN 'D' AND (RESID 164 THROUGH 179 )
34X-RAY DIFFRACTION34CHAIN 'D' AND (RESID 180 THROUGH 220 )
35X-RAY DIFFRACTION35CHAIN 'E' AND (RESID 3 THROUGH 32 )
36X-RAY DIFFRACTION36CHAIN 'E' AND (RESID 33 THROUGH 66 )
37X-RAY DIFFRACTION37CHAIN 'E' AND (RESID 67 THROUGH 86 )
38X-RAY DIFFRACTION38CHAIN 'E' AND (RESID 87 THROUGH 123 )
39X-RAY DIFFRACTION39CHAIN 'E' AND (RESID 124 THROUGH 135 )
40X-RAY DIFFRACTION40CHAIN 'E' AND (RESID 136 THROUGH 163 )
41X-RAY DIFFRACTION41CHAIN 'E' AND (RESID 164 THROUGH 179 )
42X-RAY DIFFRACTION42CHAIN 'E' AND (RESID 180 THROUGH 200 )
43X-RAY DIFFRACTION43CHAIN 'E' AND (RESID 201 THROUGH 221 )
44X-RAY DIFFRACTION44CHAIN 'F' AND (RESID 4 THROUGH 20 )
45X-RAY DIFFRACTION45CHAIN 'F' AND (RESID 21 THROUGH 66 )
46X-RAY DIFFRACTION46CHAIN 'F' AND (RESID 67 THROUGH 86 )
47X-RAY DIFFRACTION47CHAIN 'F' AND (RESID 87 THROUGH 123 )
48X-RAY DIFFRACTION48CHAIN 'F' AND (RESID 124 THROUGH 135 )
49X-RAY DIFFRACTION49CHAIN 'F' AND (RESID 136 THROUGH 163 )
50X-RAY DIFFRACTION50CHAIN 'F' AND (RESID 164 THROUGH 179 )
51X-RAY DIFFRACTION51CHAIN 'F' AND (RESID 180 THROUGH 200 )
52X-RAY DIFFRACTION52CHAIN 'F' AND (RESID 201 THROUGH 221 )
53X-RAY DIFFRACTION53CHAIN 'G' AND (RESID 3 THROUGH 20 )
54X-RAY DIFFRACTION54CHAIN 'G' AND (RESID 21 THROUGH 35 )
55X-RAY DIFFRACTION55CHAIN 'G' AND (RESID 36 THROUGH 151 )
56X-RAY DIFFRACTION56CHAIN 'G' AND (RESID 152 THROUGH 179 )
57X-RAY DIFFRACTION57CHAIN 'G' AND (RESID 180 THROUGH 221 )
58X-RAY DIFFRACTION58CHAIN 'H' AND (RESID 3 THROUGH 20 )
59X-RAY DIFFRACTION59CHAIN 'H' AND (RESID 21 THROUGH 32 )
60X-RAY DIFFRACTION60CHAIN 'H' AND (RESID 33 THROUGH 151 )
61X-RAY DIFFRACTION61CHAIN 'H' AND (RESID 152 THROUGH 179 )
62X-RAY DIFFRACTION62CHAIN 'H' AND (RESID 180 THROUGH 221 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more