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- PDB-7zhm: Salmonella enterica Rhs1 C-terminal toxin TreTu complex with TriT... -

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Basic information

Entry
Database: PDB / ID: 7zhm
TitleSalmonella enterica Rhs1 C-terminal toxin TreTu complex with TriTu immunity protein
Components
  • Immunity protein TriTu
  • Rhs1 protein
KeywordsTOXIN / Bacterial toxin / Toxin-Immunity / Secreted toxin / T6SS / Rhs
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Domain of unknown function DUF6531 / Domain of unknown function (DUF6531) / RHS protein / RHS protein / RHS repeat / RHS Repeat / PAAR motif / PAAR motif / YD repeat / Rhs repeat-associated core
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Phage protein / Rhs1 protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJurenas, D. / Rey, M. / Chamot-Rooke, J. / Terradot, L. / Cascales, E.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0039 France
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0017 France
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Salmonella antibacterial Rhs polymorphic toxin inhibits translation through ADP-ribosylation of EF-Tu P-loop.
Authors: Jurenas, D. / Rey, M. / Byrne, D. / Chamot-Rooke, J. / Terradot, L. / Cascales, E.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhs1 protein
B: Rhs1 protein
C: Immunity protein TriTu
D: Immunity protein TriTu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,06910
Polymers45,5654
Non-polymers1,5046
Water1,964109
1
A: Rhs1 protein
C: Immunity protein TriTu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5124
Polymers22,7832
Non-polymers7292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-36 kcal/mol
Surface area9970 Å2
MethodPISA
2
B: Rhs1 protein
D: Immunity protein TriTu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5586
Polymers22,7832
Non-polymers7754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-31 kcal/mol
Surface area10040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.645, 94.036, 61.305
Angle α, β, γ (deg.)90.000, 110.069, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Rhs1 protein / Type IV secretion protein Rhs


Mass: 12280.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: rhs1, AAC35_21760, D4387_21375, D5X47_21305, D6J79_20575, DLB93_21645, DNZ37_21750, DP680_20875, EBD14_21675, EBK21_05215, EPB30_20940, G0A51_20515, G0A70_20295, G0A76_24585, G0A92_21400, G0B96_ ...Gene: rhs1, AAC35_21760, D4387_21375, D5X47_21305, D6J79_20575, DLB93_21645, DNZ37_21750, DP680_20875, EBD14_21675, EBK21_05215, EPB30_20940, G0A51_20515, G0A70_20295, G0A76_24585, G0A92_21400, G0B96_23075, G0L34_19925, G0L35_16920, G0L38_12410, G0O00_10210, G0O74_11815, G0P08_23200, G3270_004033, G3A35_20815, G3V17_004532, G3V56_003855, G3V57_003909, G4202_004361, G4A85_004523, G4C74_004221, G4G97_002756, G4H00_004443, G4H24_004340, G4J08_004554, G4O67_004413, G4P85_004250, G4P93_004471, G4Q28_004357, G4Q31_004333, G4Q59_002008, G4Q60_003793, G4R01_003771, G4R15_004097, G4R16_004318, G4W86_004197, G4W87_004001, G9302_002704, G9304_004450, G9313_003832, G9367_004345, G9W65_003986, G9W79_004269, G9W95_004377, GBY13_08045, GBY73_05000, GEZ01_12865, GNB36_003912, GYI77_06060, Z700_16315
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93IR1
#2: Protein Immunity protein TriTu /


Mass: 10501.822 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_21280, A3S30_24885, A3T81_18830, A3U32_23685, A3V03_03705, A3V89_26565, A3W57_07430, A3W75_17160, A3X15_18460, A3Y76_22790, A4N07_19890, A4O05_22095, A4O41_12545, A4R48_24810, A6D61_ ...Gene: A3104_21280, A3S30_24885, A3T81_18830, A3U32_23685, A3V03_03705, A3V89_26565, A3W57_07430, A3W75_17160, A3X15_18460, A3Y76_22790, A4N07_19890, A4O05_22095, A4O41_12545, A4R48_24810, A6D61_18845, AAA76_24645, AAB27_16245, AAB79_24185, AAC35_21755, ADQ28_19745, AGM99_21090, AIT36_18185, AKH62_23030, AL144_24155, AL168_20775, AL184_23325, AQ530_17415, AU613_26795, AVA38_22450, AVL16_21415, AWT30_20335, B1265_13470, B1642_20645, B1P38_21655, B2E31_16670, B4V59_16295, B4W90_20805, B6362_18775, B7Q27_21350, B8Y16_20415, B8Z46_24695, B9C90_17255, B9C96_11800, B9M14_21175, B9O84_21965, BG493_18250, BIC00_10565, BIC13_08285, BK110_20995, BKM50_05830, BMS46_06345, BZ203_05255, BZZ88_03145, C5W43_06445, CA117_20185, CAC59_18410, CB646_20565, CBM67_18245, CBM76_20015, CBZ90_02090, CC339_16850, CC453_18020, CC652_24350, CCP17_20025, CDZ72_05380, CE70_17375, CEQ70_05720, CFF58_06395, CFF59_23420, CHN22_22420, CIX60_10615, CPS79_21305, CQO33_21175, CSG22_15055, CVR97_23495, D4361_24780, D4387_21370, D5823_18210, D5N86_25720, D5N95_24415, D5X47_21300, D6422_21315, D6J79_20570, D8S24_24495, DD95_17770, DLB93_21650, DLR28_20680, DMI89_02275, DMO92_25405, DN165_21400, DNB97_10255, DNZ37_21745, DO533_23325, DP680_20880, DPB42_24965, DPD91_20640, DPF41_22985, DPS76_24805, DQD22_24730, DQR44_25750, DRT38_21835, DSF94_24595, DU071_23735, DU657_22350, DU793_24960, DWU22_23300, DY580_17115, DYM27_14260, E0935_15085, E1A11_24660, E6W45_19865, EBD14_21680, EBK21_05210, EC404_18500, ED463_24780, EER35_24745, EHB09_18595, EK388_24345, ELS01_16950, EPB30_20945, EVY71_17715, F0D96_10735, F2P00_21530, F3Q97_07515, F3R12_08905, F9G02_19695, F9O44_23175, FEM52_19775, FGZ46_23375, FQC24_21550, G0038_13780, G0040_20120, G0042_18040, G0045_14575, G0047_13425, G0048_23400, G0051_22050, G0052_21825, G0059_15490, G0061_22165, G0062_16025, G0063_14840, G0067_13555, G0069_22925, G0070_23015, G0071_21925, G0072_07235, G0074_16430, G0076_15445, G0077_22910, G0080_17120, G0084_21735, G0086_23605, G0087_16490, G0088_22725, G0089_23720, G0090_23715, G0094_19715, G0100_23135, G0101_12940, G0102_15580, G0111_13420, G0113_17090, G0117_16475, G0123_16485, G0124_22895, G0148_15150, G0157_15905, G0170_21030, G0A32_24610, G0A39_17590, G0A43_17095, G0A44_21085, G0A46_19240, G0A50_18180, G0A51_20520, G0A53_24605, G0A58_24565, G0A60_20185, G0A61_24205, G0A66_20235, G0A67_17800, G0A68_19685, G0A70_20300, G0A73_20560, G0A76_24590, G0A79_18405, G0A92_21395, G0A96_18505, G0A97_19250, G0B03_20850, G0B05_20705, G0B07_16840, G0B08_21360, G0B12_21550, G0B96_23080, G0C03_24060, G0C04_24220, G0E15_21920, G0J24_22230, G0J26_25045, G0J27_25740, G0J28_19390, G0J31_25020, G0J33_18415, G0J34_20270, G0J36_21375, G0J37_24850, G0J40_21210, G0J43_24590, G0J44_24385, G0J45_23050, G0J46_22870, G0J47_24120, G0J49_20830, G0J51_21340, G0J53_11145, G0J55_24390, G0J58_15270, G0J66_15690, G0J67_25385, G0J69_25180, G0J71_10030, G0J76_18575, G0J79_03375, G0J81_26215, G0J82_02110, G0J85_17250, G0J97_23130, G0K00_25630, G0K02_24765, G0K03_21950, G0K04_16625, G0K05_24660, G0K07_08180, G0K13_24505, G0K15_25490, G0K18_22600, G0K20_24440, G0K23_21730, G0K25_19165, G0K26_19795, G0K30_21835, G0K31_21125, G0K32_24960, G0K33_21675, G0K37_26455, G0K38_09335, G0K39_24415, G0K41_25485, G0K42_07385, G0K44_21165, G0K46_22525, G0K47_20865, G0K56_20360, G0K61_19885, G0K65_20230, G0K68_13530, G0K70_20080, G0K72_25870, G0K75_20250, G0K78_22450, G0K83_20680, G0K84_08060, G0K88_004862, G0K89_004674, G0K90_004874, G0K94_004855, G0K95_004955, G0L00_004940, G0L02_004996, G0L03_24850, G0L06_24860, G0L07_26440, G0L10_24895, G0L14_15080, G0L15_24510, G0L18_24450, G0L19_24455, G0L20_20700, G0L24_22165, G0L25_20785, G0L29_20935, G0L31_20250, G0L32_18730, G0L34_19930, G0L35_16925, G0L36_21935, G0L37_20125, G0L38_12415, G0L48_24860, G0L49_24370, G0L51_18465, G0L52_23735, G0L55_21695, G0L59_24055, G0L62_23350, G0L63_24085, G0L65_24025, G0L67_19310, G0L68_17340, G0L73_23990, G0L76_23685, G0L78_24345, G0L79_23490, G0L83_23425, G0L86_004812, G0L89_24295, G0L91_24300, G0L96_18690, G0M05_22390, G0M06_004322, G0M13_004595, G0M14_21270, G0M16_23890, G0M18_004837, G0M21_22175, G0M22_004559, G0M25_004774, G0M26_24365, G0M29_004801, G0M30_21230, G0M33_24520, G0M35_09450, G0M38_22475, G0M39_24755, G0M41_21985, G0M45_21465, G0M46_004440, G0M48_004285, G0M53_23940, G0M55_19470, G0M56_19795, G0M58_20480, G0M63_26290, G0M65_19275, G0M67_19925, G0N45_07225, G0N48_21510, G0N51_19570, G0N53_23280, G0N55_14925, G0N57_23975, G0N58_12235, G0N59_12850, G0N60_07005, G0N61_11300, G0N62_19460, G0N64_21975, G0N65_17595, G0N66_06990, G0N67_21060, G0N71_13580, G0N75_12675, G0N78_12230, G0N82_24540, G0N84_21935, G0N85_09660, G0N86_06910, G0N88_19275, G0N89_17190, G0N90_13675, G0N94_23710, G0N95_20720, G0N98_19345, G0N99_14210, G0O00_10205, G0O10_08850, G0O14_23250, G0O19_21995, G0O20_19940, G0O22_07780, G0O25_02530, G0O27_12190, G0O31_13055, G0O32_20735, G0O37_05335, G0O39_11125, G0O40_07750, G0O41_22035, G0O42_21895, G0O43_14195, G0O47_22690, G0O52_15185, G0O55_24580, G0O57_14580, G0O58_14110, G0O59_02765, G0O60_13880, G0O63_14335, G0O68_16445, G0O70_16490, G0O71_22265, G0O74_11810, G0O75_22305, G0O77_14470, G0O78_16070, G0O80_13375, G0O81_17735, G0O82_14790, G0O84_15955, G0O85_22150, G0O87_15165, G0O89_22500, G0O92_22385, G0O93_21600, G0O97_23980, G0O99_21870, G0P00_11275, G0P01_09120, G0P02_11570, G0P06_15360, G0P08_23205, G0P12_21645, G0P13_14815, G0P17_08625, G0P18_23550, G0P19_15165, G0P24_23215, G0P26_16080, G0P28_15535, G0P30_18490, G0P31_16945, G0P36_17640, G0P37_03640, G0P41_08910, G0P44_05725, G0P45_20895, G0P48_14810, G0P49_24390, G0P52_16495, G0P53_25970, G0P56_15465, G0P57_22450, G0P58_07240, G0P65_09610, G0P69_15980, G0P73_20420, G0P75_21260, G0P76_06270, G1N61_22185, G1N64_16755, G1N66_16750, G1N68_16445, G1N71_16735, G1N72_16750, G1N86_17030, G1N87_16775, G1N91_02715, G1O00_17040, G1O02_17040, G1O04_16755, G1O05_16750, G1O08_22790, G1O10_20855, G1O12_17045, G1O16_17040, G1O17_16525, G1O18_17045, G1O20_17035, G1O23_16075, G1O25_17030, G1O26_17035, G1O27_21860, G1O28_16795, G1O29_21775, G1O32_17025, G1O34_17105, G1O38_22465, G1O40_23015, G1O43_17025, G1O46_16735, G1O48_16810, G1O49_16885, G1O51_17030, G1O53_17100, G1O62_17040, G1O63_17020, G1O65_21780, G1O67_16355, G1O68_22065, G1O69_16595, G1O71_16590, G1O72_22140, G1O76_17115, G1O77_17030, G1O80_17125, G1O81_16760, G1O83_17620, G1O84_17115, G1O87_17120, G1O88_22145, G1O89_17040, G1O90_17110, G1O93_17110, G1O94_17105, G1O96_17110, G1P02_17100, G1P03_17955, G1P06_22395, G1P09_16990, G1P10_17055, G1P12_17110, G1P14_23900, G1P15_17570, G1P17_17120, G1P19_17110, G1P23_17115, G1P24_22065, G1P25_18595, G1P26_22030, G1P29_17940, G1P31_17100, G1P35_17035, G1P36_17030, G1P37_20220, G1P40_22710, G1P44_17035, G1P45_17115, G1P47_16830, G1P48_17115, G1P51_17115, G1P52_17885, G1P53_17830, G1P54_17125, G1P55_16805, G1P56_17090, G1P57_16840, G1P58_17105, G1P59_17115, G1P61_17570, G1P64_16805, G1P67_21670, G1P69_17025, G1P72_20030, G1P75_16360, G1P76_16700, G1P78_17005, G1P83_20760, G1P84_17040, G1P87_17110, G1P90_16190, G1P91_17105, G1Q03_16720, G1Q08_21475, G1Q67_17115, G1Q78_19740, G1Q81_16595, G1Q83_17535, G1Q84_19165, G1Q85_16240, G1Q86_16210, G1Q88_20510, G1Q90_21735, G1Q91_22000, G1Q93_21400, G1Q96_25325, G1Q98_16260, G1Q99_20460, G1R01_17960, G1R02_17040, G1R03_22070, G1R04_17050, G1R08_14270, G1R13_21520, G1R15_20520, G1R20_02785, G1R21_15830, G1R22_16790, G1R23_14625, G1R27_16360, G1R28_16555, G1R29_17120, G1R30_16810, G1R31_16595, G1R36_18045, G1R38_16005, G1R40_16640, G1R42_25245, G1R44_22230, G1R45_21135, G1R47_16330, G1R48_19405, G1R51_16745, G1R53_18050, G1R63_22140, G1R69_20835, G1R87_17240, G1R93_16715, G1S02_16830, G2203_21425, G2212_15325, G2218_13260, G2279_08735, G2290_16920, G2793_20235, G2951_19065, G3221_004811, G3230_001780, G3231_003879, G3247_004837, G3248_001209, G3254_003730, G3270_004034, G3275_004813, G3336_003433, G3357_000489, G3369_004805, G3433_001837, G3464_004195, G3593_004828, G3A35_20820, G3V06_004100, G3V14_003903, G3V17_004533, G3V56_003854, G3V57_003910, G3X03_003938, G4189_003906, G4190_003784, G4192_004102, G4198_004153, G4201_001080, G4202_004362, G4A01_004238, G4A73_004743, G4A83_005114, G4A87_000956, G4B68_004665, G4B72_003508, G4B74_004047, G4C74_004222, G4D46_003776, G4F88_05850, G4F89_18520, G4F91_18175, G4F92_05850, G4G62_004887, G4G67_004167, G4G68_004801, G4G75_004042, G4G76_004048, G4G97_002755, G4H00_004444, G4H04_005144, G4H08_004806, G4H18_004810, G4H21_004803, G4H24_004341, G4H63_002715, G4I66_000598, G4J08_004555, G4J11_001980, G4J12_003329, G4J18_004322, G4J37_003944, G4J39_003448, G4J41_004178, G4J45_003829, G4J90_001468, G4K02_001147, G4K03_003353, G4O54_004070, G4O56_003838, G4O59_004025, G4O60_004234, G4O67_004414, G4O69_004025, G4P83_003986, G4P85_004251, G4P91_004016, G4P93_004472, G4Q12_004823, G4Q28_004358, G4Q31_004334, G4Q50_003968, G4Q52_003922, G4Q59_002007, G4Q60_003792, G4Q63_001067, G4Q94_004834, G4R01_003770, G4R02_004438, G4R15_004098, G4R16_004319, G4W68_004926, G4W73_004895, G4W86_004198, G4W87_004002, G4W88_004801, G4W91_004805, G4Y10_002409, G9269_004199, G9302_002703, G9305_004856, G9309_005009, G9313_003833, G9314_004703, G9367_004346, G9381_004732, G9C41_003972, G9C46_003916, G9C47_004060, G9C49_003732, G9C57_004803, G9C64_004472, G9G03_003957, G9G04_001247, G9G36_005129, G9G45_004558, G9G50_004372, G9G62_001322, G9W28_004171, G9W45_003984, G9W63_004617, G9W65_003987, G9W79_004270, G9W95_004378, G9W96_004800, GB021_10965, GB055_04415, GB076_17045, GB120_12265, GB131_19950, GB139_22990, GB171_14405, GB238_02775, GB280_14665, GB321_14460, GB331_23540, GB339_17310, GB342_18675, GB368_16270, GB372_23665, GB416_05155, GB452_17995, GB551_15365, GB567_23270, GBS44_20470, GBS58_20685, GBV53_19000, GBV54_05600, GBV60_14260, GBW44_24125, GBW52_14355, GBX12_18915, GBX20_18780, GBX46_21740, GBX55_16600, GBX64_17400, GBY13_08040, GBY23_19195, GBY73_04995, GBZ51_12855, GBZ55_24160, GCZ80_16680, GEZ01_12860, GJE27_26390, GJE28_08005, GNB28_004372, GNB36_003911, GNB86_003798, GNC11_003866, GNC19_004178, GNC45_003899, GNC75_003847, GTH60_08285, GTH62_23985, GTH63_21380, GTH68_16350, GTH70_24020, GTH73_18915, GTH75_20565, GTH77_04125, GTH78_21700, GTH79_06145, GTH81_12470, GTH85_15115, GTH87_15270, GTH89_25265, GTH90_24705, GTH91_24140, GTH93_17950, GTH94_22025, GTH99_25265, GXC51_12215, GXC56_23790, GXG40_14360, GYI62_004095, GYI77_06055, GYJ04_10830, GYJ27_02810, GYJ28_003616, GYJ30_21530, GYJ32_17670, GYJ53_17120, GYJ59_23540, GYJ60_22120, H8S97_01475, JJB80_01480, JJB81_01480, KP44_21460, NG06_24890, R035_03375, SEL4126_35730, STMLT2P22_CBEKMEGD_01031, Z700_16310, ZV17_24660, ZV33_19520, ZX03_23930, ZY40_12970
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3TET1

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Non-polymers , 4 types, 115 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.001M ZnSulfate heptahydrate; 0.05M HEPES 7.8; 28% PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.281493 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.281493 Å / Relative weight: 1
ReflectionResolution: 2.7→49.11 Å / Num. obs: 17246 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 0.974 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.11 / Rrim(I) all: 0.271 / Net I/σ(I): 5.9 / Num. measured all: 102560 / Scaling rejects: 191
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.830.7681311223020.6750.3540.8482.4100
8.95-49.110.11327724900.9890.0510.1259.998.9

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Processing

Software
NameVersionClassification
PDB-REDO5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished

Resolution: 2.7→49.11 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.886 / SU B: 22.404 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.649 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25696 894 5.2 %RANDOM
Rwork0.21376 ---
obs0.21596 16319 99.67 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.168 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å21.17 Å2
2--2.11 Å2-0 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 92 109 3385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0183346
X-RAY DIFFRACTIONr_bond_other_d0.0010.023068
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.8654544
X-RAY DIFFRACTIONr_angle_other_deg0.8992.7357104
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7125397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.66523.855166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36615573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.261514
X-RAY DIFFRACTIONr_chiral_restr0.0570.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023725
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02725
X-RAY DIFFRACTIONr_mcbond_it4.11.4631600
X-RAY DIFFRACTIONr_mcbond_other4.0811.4621599
X-RAY DIFFRACTIONr_mcangle_it5.6962.1871993
X-RAY DIFFRACTIONr_mcangle_other5.7022.1881994
X-RAY DIFFRACTIONr_scbond_it7.9772.1191746
X-RAY DIFFRACTIONr_scbond_other7.9752.1191747
X-RAY DIFFRACTIONr_scangle_other10.0532.9152552
X-RAY DIFFRACTIONr_long_range_B_refined10.9918.2883520
X-RAY DIFFRACTIONr_long_range_B_other10.97918.2623515
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 65 -
Rwork0.338 1230 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4729-1.62131.36513.3537-0.28582.6342-0.00790.0006-0.2386-0.1118-0.00990.17390.1170.02110.01780.3769-0.0098-0.12250.0061-0.01640.139639.4470.87620.888
23.8005-1.01340.45084.3216-0.79712.7578-0.06070.15760.1012-0.06290.0036-0.2297-0.18670.10220.05710.3394-0.0264-0.14570.0153-0.00320.119212.6368.864-0.398
32.5671-0.19031.15043.47061.26944.5509-0.149-0.04130.0371-0.0913-0.01350.1557-0.0255-0.25060.16250.3398-0.0187-0.13530.01630.00420.174835.04517.14532.64
42.7971.7978-0.44443.2838-0.63542.87230.0083-0.0667-0.22430.1464-0.0634-0.1847-0.05620.13210.05510.36670.0432-0.18850.0154-0.01050.13447.924-7.27911.307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2B1 - 114
3X-RAY DIFFRACTION3C1 - 87
4X-RAY DIFFRACTION4D1 - 87

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