[English] 日本語
Yorodumi
- PDB-7zg6: TacA1 antitoxin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zg6
TitleTacA1 antitoxin
ComponentsDUF1778 domain-containing protein
KeywordsANTITOXIN / Salmonella / Toxin-antitoxin system / RHH domain
Function / homologyVibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / Ribbon-helix-helix / regulation of DNA-templated transcription / DUF1778 domain-containing protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGrabe, G.J. / Morgan, R.M.L. / Helaine, S.
Funding support United Kingdom, European Union, 4items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009629/1 United Kingdom
European Research Council (ERC)757369European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D524840/1 United Kingdom
Wellcome Trust202926/Z/16/Z United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Molecular stripping underpins derepression of a toxin-antitoxin system.
Authors: Grabe, G.J. / Giorgio, R.T. / Wieczor, M. / Gollan, B. / Sargen, M. / Orozco, M. / Hare, S.A. / Helaine, S.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title
Revision 1.3Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUF1778 domain-containing protein
B: DUF1778 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8843
Polymers20,8602
Non-polymers241
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-31 kcal/mol
Surface area6760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.990, 68.990, 69.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-101-

MG

-
Components

#1: Protein DUF1778 domain-containing protein


Mass: 10429.851 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: A3104_05255, A3S30_03565, A3T81_04105, A3U32_05670, A3V03_13915, A3V89_00845, A3W57_03990, A3W75_07045, A3X15_00845, A3X55_00325, A3Y76_07970, A4N07_08005, A4O05_01325, A4O41_02030, A4R48_ ...Gene: A3104_05255, A3S30_03565, A3T81_04105, A3U32_05670, A3V03_13915, A3V89_00845, A3W57_03990, A3W75_07045, A3X15_00845, A3X55_00325, A3Y76_07970, A4N07_08005, A4O05_01325, A4O41_02030, A4R48_08935, A6D61_12035, AAA76_07485, AAB27_15580, AAB79_05115, AAC35_03625, ADQ28_10175, AF497_21965, AGM99_05600, AHN93_12130, AIT36_00965, AKH62_19105, AL144_05695, AL168_00235, AL184_01805, AQ530_13115, AU613_00250, AVA38_12925, AVC05_10875, AVL16_07530, AWT30_08430, AXX99_15530, B1265_05360, B1398_03145, B1642_07215, B1P38_10085, B2E31_12120, B4V59_11835, B4W90_05735, B6362_03215, B7Q27_05355, B8Y16_03500, B8Z46_06180, B9C90_03095, B9C96_10075, B9M14_05165, B9O84_11710, BBQ66_14315, BG493_00970, BIC00_08660, BIC13_03220, BK110_05555, BKM50_23075, BMS46_12650, BMU56_14435, BZ203_17650, BZZ88_00325, C5W43_16875, CA117_15910, CAC56_00970, CAC59_00965, CB102_05780, CB119_09125, CB198_11360, CB380_04130, CB535_00770, CB570_01825, CB646_00870, CBM67_04325, CBM76_05660, CBZ90_17945, CC339_13495, CC403_04170, CC453_00825, CC652_10795, CC971_08240, CCP17_05605, CDZ72_00830, CE70_05375, CED07_09525, CEQ70_11810, CFF58_15570, CFF59_19345, CHN22_12865, CIX60_11710, CPS79_04635, CQO33_02710, CSG22_15805, CVR97_16715, D4361_00880, D4387_02960, D4422_08010, D5823_11460, D5N86_07595, D5N95_00880, D5O82_10090, D5P17_09705, D5X47_03750, D5Y28_11875, D6422_07755, D6J79_03215, D8S24_00875, DLB93_00880, DLR28_04665, DMI89_02725, DMO92_11765, DN165_06005, DNB97_10970, DNM27_08060, DNZ37_00880, DO533_01630, DP680_00880, DPB42_14145, DPD91_14800, DPF41_20265, DPF68_06590, DPS76_07075, DQD22_06090, DQR44_03755, DRM14_09660, DRT38_10160, DRT61_12455, DRV05_07095, DSF94_03190, DSG41_05900, DTF68_09765, DU071_11260, DU223_00815, DU657_08780, DU879_06935, DUV75_05405, DWU22_19580, DY580_11365, DYM27_07925, E0935_00855, E1A11_05885, E6W45_05500, EBD14_00860, EBK21_06270, EC404_08070, EEQ30_12970, EER35_04045, EHB09_10535, EL822_04920, ELS01_06375, EPB30_06160, EQG93_08445, EVY71_04545, EW905_00790, F0D96_17675, F2P00_07215, F3Q97_08560, F3R12_09955, F9G02_14055, F9O44_13860, FE758_17770, FEM52_12105, FGZ46_08045, FJM64_04970, FQC24_05140, G0038_06515, G0040_06835, G0042_12205, G0045_10420, G0047_05575, G0048_09090, G0051_05645, G0052_10845, G0059_05920, G0061_08170, G0062_08755, G0063_08645, G0067_09250, G0069_08825, G0070_07845, G0071_07185, G0072_20045, G0074_10225, G0076_07480, G0077_09020, G0080_10875, G0084_11635, G0086_11145, G0087_09090, G0088_08175, G0089_05200, G0090_03750, G0094_03980, G0100_14430, G0101_08275, G0102_07975, G0111_07605, G0113_09075, G0117_05810, G0123_09090, G0124_08815, G0148_07850, G0157_08505, G0170_09825, G0A05_14075, G0A28_05465, G0A32_06825, G0A39_18140, G0A43_17520, G0A44_05550, G0A46_06310, G0A50_04840, G0A51_06360, G0A52_16360, G0A53_03430, G0A56_14045, G0A58_04545, G0A60_05590, G0A61_07875, G0A63_17195, G0A66_04925, G0A67_08445, G0A68_18030, G0A70_04840, G0A73_06565, G0A76_16870, G0A79_08455, G0A92_06600, G0A96_06095, G0A97_04965, G0B03_06365, G0B05_02820, G0B07_02725, G0B08_03810, G0B12_00880, G0B28_10240, G0B96_06335, G0C03_03190, G0C04_07190, G0C34_08565, G0E15_12925, G0E20_13295, G0G84_14085, G0J24_05055, G0J26_08460, G0J27_00095, G0J28_06230, G0J31_03640, G0J33_04725, G0J34_09505, G0J36_06530, G0J37_09245, G0J40_08070, G0J43_05190, G0J44_09360, G0J45_06495, G0J46_07005, G0J47_09125, G0J49_07265, G0J50_09965, G0J51_08105, G0J53_03235, G0J55_05945, G0J58_04230, G0J59_20595, G0J62_02515, G0J65_11725, G0J66_02900, G0J67_06095, G0J69_03030, G0J71_03030, G0J73_12265, G0J76_03040, G0J79_08505, G0J81_05720, G0J82_07345, G0J85_05720, G0J89_12195, G0J92_11440, G0J94_12605, G0J96_11010, G0J97_05440, G0K00_10905, G0K02_08285, G0K03_06860, G0K04_04250, G0K05_00240, G0K07_03030, G0K10_07455, G0K13_06135, G0K15_04670, G0K16_11380, G0K18_09305, G0K19_03650, G0K20_01175, G0K23_06850, G0K25_00860, G0K26_09485, G0K28_12265, G0K30_06250, G0K31_02845, G0K32_21510, G0K33_05630, G0K37_00860, G0K38_10400, G0K39_00335, G0K41_00085, G0K42_08445, G0K44_09515, G0K46_05720, G0K47_10440, G0K48_11600, G0K49_12390, G0K52_13585, G0K53_13740, G0K56_12050, G0K58_17230, G0K59_13125, G0K61_08780, G0K65_07070, G0K68_05005, G0K70_08325, G0K72_03975, G0K74_16835, G0K75_06960, G0K78_11500, G0K80_19145, G0K83_05585, G0K84_13785, G0K85_10750, G0K88_003091, G0K89_000478, G0K90_000620, G0K94_000430, G0K95_000292, G0L00_000826, G0L02_000147, G0L03_04555, G0L06_01490, G0L07_01390, G0L10_04810, G0L14_03745, G0L15_14085, G0L18_01845, G0L19_04630, G0L20_03085, G0L24_03300, G0L25_01965, G0L29_02895, G0L31_11005, G0L32_05770, G0L34_00205, G0L35_02995, G0L36_06695, G0L37_03740, G0L38_01885, G0L40_13160, G0L42_04645, G0L48_07890, G0L49_00765, G0L51_03265, G0L52_00205, G0L55_04440, G0L59_01970, G0L62_04765, G0L63_03260, G0L65_18350, G0L67_02995, G0L68_05120, G0L70_10470, G0L73_04820, G0L76_03925, G0L77_17435, G0L78_01720, G0L79_04450, G0L83_11890, G0L85_15975, G0L86_000812, G0L88_02390, G0L89_04205, G0L91_04730, G0L93_17950, G0L96_03385, G0L98_18590, G0M00_19130, G0M05_16255, G0M06_000797, G0M13_000386, G0M14_02960, G0M16_02050, G0M18_000979, G0M21_11905, G0M22_000387, G0M25_000386, G0M26_03060, G0M29_000386, G0M30_05720, G0M33_12160, G0M35_05655, G0M36_14210, G0M38_01790, G0M39_00205, G0M40_05845, G0M41_07030, G0M45_06700, G0M46_000387, G0M48_000386, G0M51_18885, G0M53_03230, G0M55_04405, G0M56_01960, G0M58_01960, G0M63_03225, G0M65_01595, G0M67_04405, G0N45_04990, G0N48_08870, G0N51_12275, G0N53_04100, G0N55_07635, G0N57_04235, G0N58_04670, G0N59_10615, G0N60_09690, G0N61_05575, G0N62_05150, G0N64_07260, G0N65_06200, G0N66_09410, G0N67_07280, G0N71_08275, G0N75_10630, G0N78_06745, G0N82_06845, G0N84_07815, G0N85_04100, G0N86_11270, G0N88_07695, G0N89_06295, G0N90_07775, G0N92_16350, G0N94_02910, G0N95_11325, G0N98_10685, G0N99_03385, G0O00_03935, G0O03_07580, G0O10_06805, G0O14_02520, G0O15_13895, G0O18_14755, G0O19_09410, G0O20_06675, G0O22_05735, G0O25_08960, G0O27_07635, G0O31_08180, G0O32_05755, G0O36_06595, G0O37_08385, G0O39_05570, G0O40_13490, G0O41_08050, G0O42_08170, G0O43_09115, G0O44_05530, G0O47_08630, G0O52_07975, G0O55_07350, G0O57_07915, G0O58_10050, G0O59_14250, G0O60_09400, G0O63_04985, G0O66_13570, G0O68_07395, G0O70_08825, G0O71_08830, G0O74_07800, G0O75_07515, G0O77_08670, G0O78_08440, G0O80_07565, G0O81_03470, G0O82_10280, G0O84_08825, G0O85_05775, G0O86_10380, G0O87_07970, G0O88_03850, G0O89_06015, G0O92_08935, G0O93_04240, G0O94_13365, G0O97_02240, G0O99_13400, G0P00_15000, G0P01_02695, G0P02_06645, G0P05_12915, G0P06_08355, G0P08_09050, G0P12_13305, G0P13_05680, G0P17_06760, G0P18_07640, G0P19_05475, G0P24_03400, G0P26_08830, G0P28_08900, G0P30_08560, G0P31_10875, G0P36_12775, G0P37_02110, G0P41_15205, G0P44_03655, G0P45_07105, G0P48_07965, G0P49_00335, G0P52_05645, G0P53_00330, G0P56_10010, G0P57_08830, G0P58_04990, G0P63_06775, G0P65_04880, G0P67_10125, G0P68_07255, G0P69_00325, G0P73_13720, G0P75_01825, G0P76_03245, G1N61_05970, G1N64_05885, G1N66_05875, G1N68_05880, G1N71_05895, G1N72_05885, G1N86_05895, G1N87_05895, G1N91_06610, G1O00_03055, G1O02_05890, G1O04_05895, G1O05_05885, G1O08_05875, G1O10_07975, G1O12_05895, G1O16_05890, G1O17_05965, G1O18_05890, G1O20_05895, G1O23_05895, G1O25_05875, G1O26_05895, G1O27_05955, G1O28_05970, G1O29_05955, G1O32_05875, G1O34_05965, G1O38_06300, G1O40_05895, G1O43_05880, G1O46_03050, G1O48_05970, G1O49_05965, G1O51_05890, G1O53_05950, G1O62_05890, G1O63_05880, G1O65_05970, G1O67_07430, G1O68_05895, G1O69_05895, G1O71_09050, G1O72_05970, G1O76_05970, G1O77_05895, G1O80_05965, G1O81_05890, G1O83_05960, G1O84_05970, G1O87_05970, G1O88_05970, G1O89_05895, G1O90_05970, G1O93_05960, G1O94_05955, G1O96_05965, G1P02_05955, G1P03_05995, G1P06_05950, G1P09_03685, G1P10_05895, G1P12_05970, G1P14_00860, G1P15_08090, G1P17_05970, G1P19_05965, G1P23_05965, G1P24_05885, G1P25_05970, G1P26_05890, G1P29_05975, G1P31_05950, G1P35_05895, G1P36_05890, G1P37_05920, G1P40_03125, G1P44_05890, G1P45_05960, G1P47_05965, G1P48_05970, G1P51_05970, G1P52_05920, G1P53_05920, G1P54_05970, G1P55_05965, G1P56_05950, G1P57_05970, G1P58_05955, G1P59_05970, G1P61_08375, G1P64_05970, G1P67_05965, G1P69_05875, G1P72_10265, G1P75_05895, G1P76_05880, G1P78_03700, G1P83_03715, G1P84_05890, G1P87_05960, G1P90_05715, G1P91_05955, G1Q03_05890, G1Q08_05185, G1Q67_05960, G1Q78_05595, G1Q81_05965, G1Q83_05970, G1Q84_05625, G1Q85_05925, G1Q86_05880, G1Q88_03055, G1Q90_05955, G1Q91_05895, G1Q93_04950, G1Q96_05860, G1Q98_05895, G1Q99_05955, G1R01_05875, G1R02_03055, G1R03_05965, G1R04_05970, G1R08_05945, G1R13_05450, G1R15_05045, G1R20_03845, G1R21_05650, G1R22_03130, G1R23_03685, G1R27_05870, G1R28_05970, G1R29_05965, G1R30_05970, G1R31_06165, G1R36_05970, G1R38_05890, G1R40_03130, G1R42_03055, G1R44_05965, G1R45_07650, G1R47_03700, G1R48_03395, G1R51_05880, G1R52_08035, G1R53_05950, G1R63_05970, G1R69_00860, G1R87_03685, G1R93_05880, G1S02_05970, G2203_08010, G2212_16670, G2218_10055, G2221_14440, G2279_12050, G2290_12650, G2793_13330, G2918_13520, G2951_06210, G3221_002687, G3230_003613, G3231_002106, G3247_003536, G3248_001297, G3254_000041, G3263_002896, G3270_003435, G3275_000730, G3312_001759, G3336_003551, G3357_001662, G3369_000598, G3433_000039, G3460_000171, G3464_002693, G3593_003627, G3A35_06005, G3V06_000996, G3V14_003115, G3V17_000446, G3V21_001922, G3V56_000559, G3V57_001798, G3X03_001804, G4189_001061, G4190_000739, G4192_000812, G4198_000464, G4201_002101, G4202_001475, G4A01_003277, G4A73_001924, G4A83_004288, G4A85_000794, G4A87_001128, G4B68_002273, G4B72_002691, G4B74_000681, G4C74_000731, G4D32_002863, G4D46_002458, G4F88_00970, G4F89_00970, G4F91_00970, G4F92_00970, G4G47_002693, G4G62_000410, G4G67_002618, G4G68_003383, G4G75_001677, G4G76_001466, G4G79_002670, G4G97_002413, G4H00_000793, G4H04_004572, G4H07_003669, G4H08_000532, G4H18_000731, G4H21_000731, G4H24_000730, G4H63_001252, G4I66_003375, G4J07_001211, G4J08_002078, G4J11_000370, G4J12_000193, G4J18_002023, G4J20_003006, G4J37_004094, G4J39_002351, G4J41_001527, G4J45_002735, G4J90_001712, G4K02_000287, G4K03_000466, G4O54_000644, G4O56_001570, G4O59_000812, G4O60_000681, G4O67_000089, G4O69_001284, G4P29_001084, G4P83_001851, G4P85_000793, G4P89_003493, G4P91_001061, G4P93_001762, G4Q12_003651, G4Q28_000730, G4Q31_000728, G4Q50_002142, G4Q52_001801, G4Q59_002806, G4Q60_000793, G4Q63_002240, G4Q67_002883, G4Q94_003297, G4R01_000792, G4R02_002284, G4R15_002694, G4R16_000737, G4W68_003700, G4W73_000555, G4W86_000984, G4W87_000730, G4W88_000730, G4W91_000171, G4Y10_003993, G9269_000834, G9302_000793, G9304_001305, G9305_003574, G9309_000405, G9313_000793, G9314_004791, G9367_001474, G9381_000651, G9C24_000382, G9C41_000996, G9C46_000850, G9C47_000681, G9C49_001054, G9C57_000728, G9C64_002283, G9G03_000497, G9G04_003111, G9G34_001926, G9G36_000577, G9G45_002412, G9G50_002044, G9G62_002044, G9W19_001373, G9W28_001671, G9W45_000065, G9W52_002689, G9W63_002268, G9W65_000728, G9W79_002140, G9W95_000731, G9W96_002672, G9X40_002429, GB021_12045, GB040_11900, GB055_08450, GB076_09505, GB106_05935, GB114_08425, GB120_05560, GB122_13965, GB131_01480, GB139_06875, GB171_04135, GB209_06840, GB221_07870, GB224_00855, GB238_15785, GB280_05645, GB321_07520, GB331_07235, GB339_13210, GB342_05095, GB368_12215, GB372_06145, GB416_14990, GB452_06040, GB459_14220, GB466_12015, GB505_11895, GB510_10150, GB551_04205, GB567_10895, GB645_16180, GBS44_03925, GBS58_06025, GBV53_06495, GBV54_10940, GBV60_02935, GBW03_15445, GBW44_14930, GBW52_04530, GBW76_13765, GBX12_15340, GBX20_14950, GBX46_08290, GBX55_07645, GBX64_03960, GBY13_11225, GBY23_15345, GBY73_06075, GBZ51_19885, GBZ55_00575, GCZ80_15175, GEZ01_02980, GJE27_05655, GJE28_04530, GNA88_002718, GNA97_002865, GNA99_002432, GNB28_002419, GNB36_000624, GNB86_001092, GNC11_000727, GNC19_001070, GNC45_001165, GNC75_002133, GNC95_001305, GT380_05455, GTH60_03850, GTH62_02950, GTH63_08330, GTH66_08435, GTH67_11860, GTH68_08760, GTH70_03975, GTH72_08690, GTH73_05575, GTH75_06305, GTH77_02135, GTH78_08775, GTH79_06410, GTH81_13490, GTH85_09070, GTH87_09400, GTH89_05040, GTH90_06140, GTH91_00195, GTH93_08825, GTH94_05825, GTH99_03645, GXC51_05525, GXC56_05525, GXG40_05525, GYI58_17275, GYI62_000736, GYI77_09250, GYJ04_02110, GYJ24_05825, GYJ27_19115, GYJ28_003979, GYJ30_10035, GYJ32_11340, GYJ53_05965, GYJ59_05485, GYJ60_05955, H8S97_18675, JJB80_18360, JJB81_18355, KP44_05620, NG06_06920, R035_07945, Z700_03565, ZV17_16945, ZV33_03590, ZX03_04645, ZY40_05085
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2J0RDY6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% Tryptone 1mM Sodium azide 50mM HEPES pH 7.0 12% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.94→34.5 Å / Num. obs: 9080 / % possible obs: 99.3 % / Redundancy: 5 % / Biso Wilson estimate: 46.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.024 / Rrim(I) all: 0.055 / Net I/σ(I): 14.3
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.076 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 475 / CC1/2: 0.655 / Rpim(I) all: 0.52 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AK7

7ak7


Resolution: 1.95→34.49 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 36.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 416 4.64 %RANDOM
Rwork0.1974 8540 --
obs0.1999 8956 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.28 Å2 / Biso mean: 56.4175 Å2 / Biso min: 32.3 Å2
Refinement stepCycle: final / Resolution: 1.95→34.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 1 47 862
Biso mean--94.05 64.45 -
Num. residues----104
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.230.3021580.27728443002100
2.23-2.810.29831340.24172828296299
2.81-34.490.23371240.1782868299299

+
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://pdbjlvh1.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