[English] 日本語
Yorodumi
- PDB-7rrj: Crystal structure of fast switching M159Q mutant of fluorescent p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rrj
TitleCrystal structure of fast switching M159Q mutant of fluorescent protein Dronpa (Dronpa2)
ComponentsFluorescent protein DronpaFluorescence
KeywordsFLUORESCENT PROTEIN / Dronpa2
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / identical protein binding / metal ion binding / Fluorescent protein Dronpa
Function and homology information
Biological speciesEchinophyllia sp. SC22 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)GM118044 United States
National Science Foundation (NSF, United States)CHE-1740645 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme.
Authors: Lin, C.Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.
History
DepositionAug 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_torsion / 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)231,9098
Polymers231,9098
Non-polymers00
Water15,205844
1
A: Fluorescent protein Dronpa
C: Fluorescent protein Dronpa
E: Fluorescent protein Dronpa
G: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,9544
Polymers115,9544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fluorescent protein Dronpa
D: Fluorescent protein Dronpa
F: Fluorescent protein Dronpa
H: Fluorescent protein Dronpa


Theoretical massNumber of molelcules
Total (without water)115,9544
Polymers115,9544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.745, 85.789, 144.045
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Fluorescent protein Dronpa / Fluorescence


Mass: 28988.604 Da / Num. of mol.: 8 / Mutation: M159Q
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.: 844 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.1 M Tris-HCl pH 7.4, 0.1 M MgCl2, 18% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.198→37.742 Å / Num. obs: 96708 / % possible obs: 93.3 % / Redundancy: 12.4 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.268 / Net I/σ(I): 10.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.86 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 6925 / % possible all: 68.4

-
Processing

Software
NameVersionClassification
PHENIX1.13RC2_2986refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UTS
Resolution: 2.2→36.89 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 4600 5 %
Rwork0.242 --
obs0.243 91976 93.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→36.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14054 0 0 844 14898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514803
X-RAY DIFFRACTIONf_angle_d1.06219986
X-RAY DIFFRACTIONf_dihedral_angle_d6.22912019
X-RAY DIFFRACTIONf_chiral_restr0.0762022
X-RAY DIFFRACTIONf_plane_restr0.0052605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.22320.40281260.34422368X-RAY DIFFRACTION87
2.2232-2.24940.4241240.37152365X-RAY DIFFRACTION84
2.2494-2.27680.3588870.32631609X-RAY DIFFRACTION85
2.2768-2.30560.34541370.30352618X-RAY DIFFRACTION89
2.3056-2.33590.32861550.27282989X-RAY DIFFRACTION96
2.3359-2.36790.27341600.26593041X-RAY DIFFRACTION99
2.3679-2.40180.29411630.26163071X-RAY DIFFRACTION99
2.4018-2.43760.33231620.26393099X-RAY DIFFRACTION99
2.4376-2.47570.29471610.27563053X-RAY DIFFRACTION99
2.4757-2.51630.31021630.27323089X-RAY DIFFRACTION99
2.5163-2.55960.33951600.27033044X-RAY DIFFRACTION99
2.5596-2.60620.35311620.27513070X-RAY DIFFRACTION99
2.6062-2.65630.28851560.26783000X-RAY DIFFRACTION96
2.6563-2.71050.32461540.29682899X-RAY DIFFRACTION94
2.7105-2.76940.30381600.26473052X-RAY DIFFRACTION97
2.7694-2.83380.32311540.26292943X-RAY DIFFRACTION95
2.8338-2.90470.2741600.27253038X-RAY DIFFRACTION98
2.9047-2.98320.27251610.25853086X-RAY DIFFRACTION98
2.9832-3.07090.33221630.25693093X-RAY DIFFRACTION98
3.0709-3.170.31081620.25623057X-RAY DIFFRACTION98
3.17-3.28320.26851580.24473017X-RAY DIFFRACTION97
3.2832-3.41460.27211590.24583026X-RAY DIFFRACTION97
3.4146-3.56990.32541570.2472963X-RAY DIFFRACTION95
3.5699-3.75790.25291520.23032863X-RAY DIFFRACTION92
3.7579-3.99310.2121540.22362934X-RAY DIFFRACTION94
3.9931-4.30110.24821580.20022991X-RAY DIFFRACTION95
4.3011-4.73310.18721570.18862979X-RAY DIFFRACTION95
4.7331-5.41630.20641560.1932937X-RAY DIFFRACTION93
5.4163-6.81740.23881610.21543056X-RAY DIFFRACTION97
6.8174-36.890.20591580.21153026X-RAY DIFFRACTION93
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)
17.96850.3302-1.23712.78570.25021.89840.15640.3831-0.3593-0.3817-0.2033-0.5036-0.23310.5645-0.09450.3942-0.06330.00240.5280.07820.323829.34417.59848.072
22.92460.02910.23731.3810.41570.9540.02990.18210.0503-0.1252-0.1023-0.1085-0.08730.30720.08090.2896-0.04880.02320.3180.0350.240827.27517.00954.333
34.20770.6060.55319.1833-1.84095.7176-0.4164-0.02611.31410.11250.01620.7413-0.5394-0.3337-0.00420.24040.062-0.07780.17290.02380.4027.72925.50561.764
42.751-3.34470.60184.8119-1.58850.9938-0.01840.0797-0.050.1729-0.06780.5029-0.24870.30530.090.2719-0.0488-0.02120.3343-0.09090.320126.16416.31367.292
54.3572-2.5956-1.52694.32042.96682.7815-0.129-0.2129-0.19210.07370.07050.1377-0.07460.2386-0.00610.313-0.03870.04330.29130.02230.239427.41512.8764.62
61.8601-2.29482.42342.8157-3.24213.74560.072-0.20180.4636-0.1269-0.1734-0.3407-0.19580.12830.22830.3535-0.15270.02350.3802-0.00760.32229.48725.81660.162
75.39870.3536-1.21192.0193-0.3761.183-0.19250.3068-0.2934-0.3807-0.0608-0.21440.02920.39110.02810.3486-0.06590.10670.46550.10510.183834.95721.012-23.719
81.08980.1886-0.29771.038-0.37361.8940.00810.3289-0.046-0.1107-0.00510.0657-0.14360.1597-0.0070.2646-0.00530.01990.22850.04740.259131.98120.831-15.194
93.6937-3.1431-0.93143.92991.17221.9327-0.09390.18330.06930.1392-0.0926-0.09730.0377-0.02950.22090.28090.00320.03280.20170.06480.274533.24616.933-6.418
103.676-1.46091.88874.8203-3.25644.5198-0.15550.11740.7541-0.1364-0.1217-0.4053-0.38040.45050.23660.3637-0.11080.01730.2774-0.03660.268935.68629.119-11.684
114.71523.9496-1.08427.3586-2.02583.13290.2697-0.6082-0.22010.3494-0.37940.05720.2135-0.007-0.01930.3406-0.09690.08020.444-0.00240.2797-1.5641.84199.022
121.15560.36451.47011.33770.93282.05410.4148-0.8676-0.010.1207-0.32930.3824-0.2603-0.6120.1170.4904-0.17980.14110.6296-0.06750.2003-5.2455.54697.831
132.4170.4704-0.11895.5432-2.69051.3929-0.1397-0.19310.0388-0.01610.4788-0.1051-0.0023-0.3743-0.21570.3677-0.14370.04610.4898-0.06780.287-0.9789.28491.441
141.97430.2761-0.22953.2711-0.1171.68640.129-0.2041-0.10130.193-0.1776-0.00610.2864-0.25050.04510.3037-0.0560.01550.3744-0.00090.21782.2062.51988.108
156.2343-5.00572.01094.0965-2.15684.65190.55410.5027-0.2031-0.3094-0.57720.14220.5574-0.22690.05260.2923-0.02050.09080.31690.01860.35091.9454.79279.889
161.7957-0.80291.04743.1954-2.42355.284-0.01630.13810.29070.4079-0.2134-0.2245-0.4697-0.19150.1850.3498-0.07790.11720.3981-0.05770.22012.4858.31181.149
172.2020.111.09451.6990.37141.78440.1595-0.2433-0.2982-0.3820.10540.2650.1132-0.1756-0.19870.3877-0.17310.09050.3980.03870.2999-2.833-3.06484.989
180.7920.01220.51150.05830.18460.3374-0.0358-0.20810.0383-0.2467-0.230.5394-0.1912-0.53490.13980.4979-0.07560.09730.5761-0.0330.3503-11.0621.89984.205
193.59270.5547-0.97162.5722-0.49153.0710.278-0.38030.00410.339-0.3470.40380.3636-0.35930.01160.3186-0.13420.08370.3672-0.04720.23475.17.08327.552
201.26290.2781-0.00182.02490.34550.76460.0371-0.12590.05390.1131-0.07690.05980.0377-0.24630.03520.2326-0.080.03520.2621-0.02090.27566.9286.0816.013
211.62930.85351.19551.87530.76511.4374-0.1583-0.14530.20950.57950.1804-0.12030.2053-1.19570.3280.0628-0.42610.22410.48710.0380.4324-4.4634.87412.635
224.15572.16320.95482.28210.04073.42120.3847-0.61370.1660.2358-0.42930.0886-0.11640.4360.02960.3644-0.1356-0.02640.4699-0.01420.2128.25716.49699.337
234.40074.1204-3.82094.2072-3.59533.24610.3544-0.11250.12510.4714-0.31740.0601-0.62120.55760.11940.4609-0.1089-0.04530.69530.14380.297534.67317.09396.735
241.9595-0.04760.62142.8997-0.13640.90920.27360.07560.02920.5182-0.24290.0125-0.31950.35960.00360.3239-0.1495-0.0310.35560.0740.197327.69310.5491.803
251.82010.8581-0.28732.98770.20142.10470.0738-0.08420.2410.1461-0.33150.0611-0.37230.25220.1740.2773-0.0831-0.06590.33150.0370.196425.49324.25487.143
263.67033.21631.97296.7434.13575.94190.0979-0.33980.21920.2841-0.23990.4323-0.29650.1592-0.00750.3165-0.0933-0.00520.38280.11780.21122.41218.3996.697
271.05371.6463-0.54135.5694-0.87611.97710.1883-0.0826-0.11080.2027-0.3486-0.0392-0.01650.43510.14310.20320.02310.00820.28530.0550.211325.229.08882.346
282.6754-3.7355-1.59248.37762.76242.67890.12380.14770.15150.1588-0.15450.00520.21860.07360.08680.3354-0.1411-0.00110.33330.03060.246124.52613.35880.704
292.7014-1.3979-0.03773.8053-0.85321.0654-0.0683-0.47950.4905-0.32830.1695-0.7416-0.14760.2066-0.1260.3364-0.1049-0.05130.3782-0.01630.280329.70523.19984.976
301.5678-0.5924-0.20490.32330.21370.36360.2001-0.2159-0.10190.3687-0.218-0.1536-0.46570.95450.12220.4237-0.121-0.04670.46050.01980.31437.92118.40184.299
312.53941.37450.66724.15731.16622.26760.0762-0.1844-0.02720.2871-0.0188-0.1084-0.10550.33630.04160.2499-0.0371-0.01830.30520.0170.205935.83717.31624.813
321.16340.42-0.64652.51920.1141.20080.1678-0.21290.11920.3247-0.20020.1398-0.18880.18930.10490.3882-0.1331-0.01710.3362-0.03260.288430.56925.04519.223
333.2773-0.52420.68993.8907-0.74111.99190.1864-0.089-0.12380.1795-0.2373-0.23370.19470.3086-0.06030.1753-0.0337-0.00230.2406-0.0640.158231.52612.02510.628
343.4202-3.1452-3.82333.5143.88164.40990.128-0.1239-0.0256-0.57190.0643-0.014-0.37510.0454-0.06140.1636-0.0226-0.02690.24310.0030.229530.78716.5988.855
351.1973-0.29790.38312.4883-1.84452.42090.06160.00380.13490.0535-0.2985-0.52210.00830.46320.16130.2376-0.1226-0.01560.2687-0.02960.299338.58721.40216.447
360.0020.0315-0.0640.1709-0.39150.8591-0.54370.05140.50120.4855-0.39870.1589-0.08610.0340.12310.5577-0.3309-0.08110.5361-0.0660.599547.79635.403-2.443
374.0597-0.13170.02931.4573-0.48792.8012-0.18720.9978-0.2557-0.17290.22590.13880.3484-0.126-0.21440.3513-0.0939-0.00350.33440.00630.3355-1.432.24948.092
384.8887-0.60510.74851.2401-0.22641.1979-0.18490.0172-0.1252-0.0323-0.0620.17310.3484-0.27560.24140.4256-0.14320.00120.3724-0.07580.27232.493-2.452.043
392.1244-0.25290.08975.4246-0.17326.9991-0.17890.20330.2858-0.08140.15470.8230.0408-0.49070.00680.2287-0.0408-0.05940.5016-0.01370.4034-13.6688.57958.503
406.9042-6.19966.64055.8196-5.83847.1624-0.16220.28710.08250.4411-0.03350.0802-0.32860.0130.17190.3252-0.01990.03850.2305-0.04880.25867.1326.41661.838
415.2448-1.32423.98122.7149-1.86025.2418-0.15130.5724-0.0334-0.42830.0149-0.05210.1098-0.01050.13130.3147-0.05530.04390.2652-0.05030.30081.7696.9350.384
429.16975.4398-1.30186.5535-1.36926.716-0.56440.057-0.53390.02050.2059-0.79050.6090.5860.28170.27120.1342-0.00690.3084-0.06980.397719.203-5.34761.996
432.5219-3.47-0.20855.1621.17961.3265-0.06540.03150.03390.1087-0.0497-0.24490.3957-0.25190.12560.3493-0.05610.03820.30280.00360.24530.8923.61167.276
443.5017-2.00360.75573.8275-2.08972.79490.07420.1364-0.0171-0.1695-0.29810.28430.1857-0.19250.25620.3671-0.0357-0.0120.2681-0.09130.2447-0.4037.30664.49
451.8078-1.7039-1.1981.79350.57961.75650.133-0.0113-0.7610.2086-0.30240.59040.8003-0.53340.39470.4632-0.2408-0.01390.4421-0.05630.42091.034-7.49758.312
460.9627-0.3674-0.2340.3763-0.24320.72510.0486-0.1044-0.4322-0.16020.06720.66340.4079-0.47190.06940.1941-0.35360.06210.4294-0.23410.5069-6.928-3.68262.401
477.13730.55081.46442.315-0.25823.642-0.02320.77690.3235-0.1658-0.07520.2151-0.3469-0.59770.14830.46570.0153-0.03570.3752-0.05850.22915.0795.13-23.673
489.2047-0.1939-0.76822.334-0.05252.1092-0.3520.4295-0.2623-0.39330.33560.14020.5729-0.2310.02190.4165-0.0164-0.02450.3098-0.02870.29019.3730.247-20.06
491.56380.47150.06041.5255-0.42651.0766-0.02450.13940.0216-0.1585-0.01860.11950.126-0.20550.01810.21970.0155-0.03170.212-0.0230.2477.4327.764-12.794
507.3044-5.18754.04554.7516-4.4614.4732-0.194-0.22570.02760.28840.17850.2809-0.08040.0272-0.01660.2693-0.01860.00920.2373-0.07030.283311.1595.46-5.23
511.20390.3809-0.70470.56060.98053.1901-0.0424-0.2945-0.14050.06270.04930.33330.3123-0.70150.18920.2356-0.0975-0.05840.29830.00850.40440.056.565-9.786
524.368-0.5448-2.79244.17512.29514.6246-0.01720.333-0.58-0.5282-0.23650.29770.0722-0.50050.13930.294-0.0837-0.06720.2850.01150.30014.005-3.035-12.036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:20 )
2X-RAY DIFFRACTION2(CHAIN A AND RESID 21:123 )
3X-RAY DIFFRACTION3(CHAIN A AND RESID 124:135 )
4X-RAY DIFFRACTION4(CHAIN A AND RESID 136:163 )
5X-RAY DIFFRACTION5(CHAIN A AND RESID 164:188 )
6X-RAY DIFFRACTION6(CHAIN A AND RESID 189:220 )
7X-RAY DIFFRACTION7(CHAIN B AND RESID 4:20 )
8X-RAY DIFFRACTION8(CHAIN B AND RESID 21:151 )
9X-RAY DIFFRACTION9(CHAIN B AND RESID 152:188 )
10X-RAY DIFFRACTION10(CHAIN B AND RESID 189:220 )
11X-RAY DIFFRACTION11(CHAIN C AND RESID 5:20 )
12X-RAY DIFFRACTION12(CHAIN C AND RESID 21:46 )
13X-RAY DIFFRACTION13(CHAIN C AND RESID 47:66 )
14X-RAY DIFFRACTION14(CHAIN C AND RESID 67:151 )
15X-RAY DIFFRACTION15(CHAIN C AND RESID 152:163 )
16X-RAY DIFFRACTION16(CHAIN C AND RESID 164:179 )
17X-RAY DIFFRACTION17(CHAIN C AND RESID 180:200 )
18X-RAY DIFFRACTION18(CHAIN C AND RESID 201:226 )
19X-RAY DIFFRACTION19(CHAIN D AND RESID 3:32 )
20X-RAY DIFFRACTION20(CHAIN D AND RESID 33:200 )
21X-RAY DIFFRACTION21(CHAIN D AND RESID 201:228 )
22X-RAY DIFFRACTION22(CHAIN E AND RESID 2:32 )
23X-RAY DIFFRACTION23(CHAIN E AND RESID 33:46 )
24X-RAY DIFFRACTION24(CHAIN E AND RESID 47:66 )
25X-RAY DIFFRACTION25(CHAIN E AND RESID 67:99 )
26X-RAY DIFFRACTION26(CHAIN E AND RESID 100:123 )
27X-RAY DIFFRACTION27(CHAIN E AND RESID 124:151 )
28X-RAY DIFFRACTION28(CHAIN E AND RESID 152:179 )
29X-RAY DIFFRACTION29(CHAIN E AND RESID 180:200 )
30X-RAY DIFFRACTION30(CHAIN E AND RESID 201:228 )
31X-RAY DIFFRACTION31(CHAIN F AND RESID 3:66 )
32X-RAY DIFFRACTION32(CHAIN F AND RESID 67:123 )
33X-RAY DIFFRACTION33(CHAIN F AND RESID 124:151 )
34X-RAY DIFFRACTION34(CHAIN F AND RESID 152:179 )
35X-RAY DIFFRACTION35(CHAIN F AND RESID 180:216 )
36X-RAY DIFFRACTION36(CHAIN F AND RESID 217:228 )
37X-RAY DIFFRACTION37(CHAIN G AND RESID 3:20 )
38X-RAY DIFFRACTION38(CHAIN G AND RESID 21:66 )
39X-RAY DIFFRACTION39(CHAIN G AND RESID 67:86 )
40X-RAY DIFFRACTION40(CHAIN G AND RESID 87:99 )
41X-RAY DIFFRACTION41(CHAIN G AND RESID 100:123 )
42X-RAY DIFFRACTION42(CHAIN G AND RESID 124:135 )
43X-RAY DIFFRACTION43(CHAIN G AND RESID 136:163 )
44X-RAY DIFFRACTION44(CHAIN G AND RESID 164:188 )
45X-RAY DIFFRACTION45(CHAIN G AND RESID 189:205 )
46X-RAY DIFFRACTION46(CHAIN G AND RESID 206:220 )
47X-RAY DIFFRACTION47(CHAIN H AND RESID 3:20 )
48X-RAY DIFFRACTION48(CHAIN H AND RESID 21:66 )
49X-RAY DIFFRACTION49(CHAIN H AND RESID 67:151 )
50X-RAY DIFFRACTION50(CHAIN H AND RESID 152:179 )
51X-RAY DIFFRACTION51(CHAIN H AND RESID 180:200 )
52X-RAY DIFFRACTION52(CHAIN H AND RESID 201:219 )

+
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