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- PDB-6zii: Structure of the isolated REC domain of RcsB from Salmonella ente... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6zii | |||||||||||||||
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Title | Structure of the isolated REC domain of RcsB from Salmonella enterica serovar Typhimurium in the presence of phosphomimetic BeF3- | |||||||||||||||
![]() | Transcriptional regulatory protein RcsB | |||||||||||||||
![]() | DNA BINDING PROTEIN / response regulator / phosphorylation / two-component systems / transcriptional factor | |||||||||||||||
Function / homology | ![]() phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Huesa, J. / Marina, A. / Casino, P. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based analyses of Salmonella RcsB variants unravel new features of the Rcs regulon. Authors: Huesa, J. / Giner-Lamia, J. / Pucciarelli, M.G. / Paredes-Martinez, F. / Portillo, F.G. / Marina, A. / Casino, P. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 70.9 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6zilC ![]() 6zixC ![]() 6zj2C ![]() 5o8zS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15768.307 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: rcsB, A2O69_13765, A3042_19525, A3104_15245, A3111_09650, A3122_12425, A3146_09020, A3R41_09960, A3S30_08650, A3T21_09515, A3T81_14325, A3U32_14885, A3V03_11040, A3V89_10805, A3W57_14915, A3W75_ ...Gene: rcsB, A2O69_13765, A3042_19525, A3104_15245, A3111_09650, A3122_12425, A3146_09020, A3R41_09960, A3S30_08650, A3T21_09515, A3T81_14325, A3U32_14885, A3V03_11040, A3V89_10805, A3W57_14915, A3W75_12230, A3W86_06130, A3X15_13890, A3X55_20780, A3Y76_07040, A3Z96_14340, A4J27_11660, A4N07_14810, A4O05_20855, A4O41_07785, A4R48_08340, A6D61_15370, A9C21_06135, A9R92_21345, A9T39_16135, A9U46_10475, A9U64_21675, A9U69_21545, AAA76_10930, AAB27_22280, AAB39_09270, AAB79_16325, AAC08_11475, AAC35_11250, AAC42_16960, AAC44_14685, AAC95_13155, AAC98_10995, AAK29_10400, AAP89_11275, AAQ24_16295, AB424_18490, ABO94_17915, ABP11_15160, ABP87_18790, ABQ69_20575, ADQ28_04890, ADQ45_05825, AE787_14130, AF480_10895, AF488_12145, AF489_17255, AF497_17465, AGC55_06475, AGM99_13695, AGQ32_04375, AH984_14180, AHN93_10200, AIC76_12470, AKH62_06605, AKH68_10310, AKI16_13295, AL144_14225, AL151_13230, AL166_17425, AL168_14180, AL170_15835, AL174_14280, AL184_16885, APP08_20700, APY91_13970, AQ530_14880, AQ536_13855, AS118_05400, AT354_14865, AU613_13115, AU731_17745, AU805_14740, AU830_17945, AU839_16960, AU951_10785, AU965_14440, AVA38_10850, AVB77_17860, AVB94_12475, AVC05_13710, AVC09_15555, AVD08_14940, AVD75_10490, AVD94_16345, AVG17_17440, AVL02_06935, AVL16_12105, AVM19_11045, AWT30_16365, AXM10_15020, AXM23_15980, AXR84_09155, AXU58_12665, AXX99_08590, B1265_14695, B1398_15040, B1642_12470, B1B86_13860, B1B89_12995, B1I91_14010, B1P38_06210, B1Q82_08785, B2E31_12855, B4V59_14365, B4W90_11945, B5A40_18175, B6362_19530, B6G98_09840, B6M25_12470, B6M43_11445, B7071_09685, B7890_16815, B7J30_08950, B7Q27_13330, B8Y16_13920, B8Y36_10435, B8Z46_12215, B9653_08735, B9C61_09460, B9C71_10305, B9C90_09140, B9C91_11100, B9C96_06975, B9M14_15255, B9O84_06255, B9U29_20160, BBQ66_07980, BEL47_15520, BFE55_17500, BFE61_13600, BGP52_15605, BIC00_11775, BIC01_03425, BIC03_12465, BIC13_09510, BJP89_14935, BK110_11970, BKM50_13625, BLB03_12065, BMG85_01485, BMS46_14205, BMU56_10065, BSC80_16315, BSD55_15985, BZ203_13370, BZ210_08250, BZG47_14895, BZN20_13125, BZZ88_21635, C4E88_11520, C5U54_24325, C5W43_17645, CA117_14980, CB102_02675, CB119_10390, CB161_08930, CB198_19420, CB380_13295, CB383_12585, CB416_11695, CB530_12435, CB535_09465, CB570_05200, CB646_09025, CB657_11330, CBH20_11220, CBM40_08545, CBM67_14430, CBM76_12750, CBN77_20665, CBO42_14460, CBR08_08850, CBU15_19945, CBU32_00760, CBZ90_12320, CC339_03310, CC403_05060, CC453_12125, CC594_20855, CC652_11600, CC725_10110, CC886_11620, CC918_07450, CC944_09505, CC971_10010, CCF93_15515, CCP17_10715, CCW27_14410, CD48_15270, CD977_10835, CDJ75_08265, CDQ60_11320, CDT37_13185, CDZ72_16490, CE355_08040, CE615_16735, CE70_14835, CE806_10370, CE87_12900, CE896_01015, CEC46_09750, CEC56_04870, CED07_06500, CEL48_20705, CEL55_09205, CEQ70_15765, CER78_12570, CET98_13495, CEY64_16305, CFB16_15760, CFB28_17680, CFE76_19020, CFE79_15610, CFF58_13355, CFF59_13510, CFJ48_12690, CGG73_15810, CHN22_08020, CI444_12440, CIX60_15545, CJC42_16545, CPR79_14100, CPS79_08255, CPX68_07570, CQE35_07160, CQG18_09040, CQO33_12635, CR370_10310, CRB02_10290, CSG22_12970, CVR97_09845, D3147_17580, D3174_01810, D3F31_11215, D3T68_22780, D3Y48_14800, D4361_11425, D4369_10470, D4380_14255, D4387_10710, D4422_10715, D4E62_15595, D4E68_12645, D4E74_04805, D4X64_11635, D4X79_12705, D4Y62_12305, D5823_23275, D5949_13360, D5B48_08355, D5C67_13450, D5C71_13810, D5N86_08445, D5N95_12575, D5O82_10940, D5P17_11555, D5X47_11830, D5X51_21070, D5Y28_05580, D6360_11195, D6367_13185, D6371_12525, D6373_13850, D6395_09765, D6421_13000, D6422_12760, D6J79_14230, D6K10_23715, D6P67_11555, D6Q64_13765, D6S43_13075, D6T00_11290, D6T40_07430, D7F20_11320, D7H43_01075, D7N92_12075, D7O44_13065, D8Q90_09500, D8S24_13515, D9O84_14155, DD95_02420, DJ388_15095, DJ702_13640, DK061_07980, DK631_02345, DK641_19375, DK642_13375, DK689_12355, DK696_07780, DK698_07265, DKJ10_12345, DKR95_07440, DKS55_11340, DKU45_11320, DKU57_10630, DKU80_05405, DLB14_07805, DLB57_08870, DLB93_12855, DLR28_13470, DM322_20130, DM733_21940, DMI89_06860, DMO92_13710, DMV40_11670, DMZ93_22620, DN165_13395, DN204_13780, DN359_20245, DNB97_22830, DNL62_12910, DNM27_08910, DNM63_11945, DNU59_10640, DNV08_13515, DNV12_21330, DNV30_09985, DNY92_08010, DNZ37_12590, DO350_10650, DO533_09745, DO585_12725, DO640_13295, DO698_21090, DO766_09590, DO828_16445, DO960_04625, DOC60_14865, DOH72_12230, DOI32_09640, DOI53_11380, DOI92_10015, DOJ39_13330, DOJ91_15905, DOQ54_10850, DOQ88_19075, DOR12_10695, DOV43_19010, DOW25_10390, DP680_11760, DPB42_06345, DPB45_09375, DPB48_12795, DPB57_11855, DPD91_07890, DPD95_08365, DPD99_18580, DPF41_10345, DPF68_09290, DPJ93_06885, DPK32_10835, DPK79_10855, DPL02_08725, DPP13_16840, DPP94_12530, DPP97_14020, DPS76_08870, DPT18_10485, DPU20_11590, DPY58_18740, DQ848_10815, DQ947_12275, DQ951_12780, DQC39_14690, DQC52_17465, DQD03_12025, DQD22_14205, DQE64_12330, DQE65_13455, DQK42_17635, DQQ98_14965, DQR10_20350, DQR44_12005, DQR61_11120, DQS14_10375, DQY10_09140, DQZ46_08550, DQZ56_12760, DR982_22020, DRL45_07940, DRM14_11520, DRM16_14710, DRR75_23095, DRT38_13015, DRT61_23690, DRT65_15310, DRV05_08945, DRW84_11665, DRX36_22780, DRX66_07345, DS270_18375, DS296_03655, DS451_17430, DS453_12950, DS521_10015, DS619_11600, DSF69_12145, DSF94_10460, DSG41_14570, DSM38_11155, DSN15_12590, DSR36_10905, DTE73_10415, DTF68_07740, DTG22_22525, DTG27_16445, DTW13_10745, DTW14_14950, DTW26_11965, DU071_21905, DU223_06195, DU657_07745, DU821_10140, DU879_10520, DU924_08500, DUQ28_11140, DUQ56_08490, DUQ92_13185, DUR36_14185, DUV75_15260, DUW10_15950, DUW48_09895, DVF14_11920, DVF88_08270, DVG01_14360, DVZ53_05935, DWU22_23860, DWU62_21645, DY580_21440, DYM27_06865, DYS82_09690, DZG11_20930, E0584_16370, E0595_14185, E0600_21890, E0935_14485, E0989_09310, E0M34_15895, E0S07_16310, E0U75_13640, E0V94_09045, E1336_08925, E1A11_13485, E1A20_12000, E5196_05695, E6W45_14470, EBB93_17635, EBC01_10965, EBD14_12205, EBD99_18850, EBK21_14930, EBL31_09840, EBO41_09410, EBP31_06115, EC404_15850, EC52_15480, ECA50_20460, ECC89_11785, ED424_08285, ED467_11830, EDL18_13765, EEK73_13190, EEQ30_16240, EER35_07340, EGL32_12130, EGN81_07495, EGU67_13655, EGU98_14315, EHB09_14460, EHB24_11945, EHB55_22345, EHC98_05345, EIE48_10505, EIW53_04795, EJI18_11350, EJO08_13340, EJO98_13625, EKA25_12980, EL822_07390, ELO47_09560, ELR28_08900, ELS01_12400, EM832_12680, EM840_06380, EMN66_07620, EMY79_09360, EO190_08315, EP115_18440, EP446_20135, EPB30_13505, EPH81_08120, EQG93_05510, EQG94_13030, ERM04_09810, EU306_11875, EU349_11640, EU873_21965, EUB95_05675, EUQ56_12115, EUQ65_09175, EUQ74_13570, EUS13_08790, EVT69_22445, EVY71_04215, EW905_06135, EWB18_06485, EWE52_05820, EWJ47_09340, EWZ09_13550, EXA47_07665, EXB31_05300, EXB41_09095, EYA29_15940, EYJ91_08825, F0D96_14965, F2O93_14305, F2P00_11865, F3Q46_16675, F3Q58_07850, F3Q59_15070, F3Q88_00720, F3Q97_16025, F3R12_18690, F3R61_10195, F3R63_13520, F9G02_06435, F9O44_04025, FE758_13940, FEM52_13990, FGZ46_08850, FJM64_14760, FL833_11895, FQC24_10010, FQD13_04095, FQX78_02535, GCH31_06840, GCQ81_17295, GCZ80_15980, GEZ01_10265, GW08_14750, JO10_24665, KP44_13855, LZ63_14980, NCTC13348_05301, NG02_14230, NG06_18895, NG18_08765, NU83_17610, QA89_08030, QB40_11485, QD15_11360, R035_06990, RJ78_11590, SAMEA4398682_01637, SE14_02481, Y934_23370, YG50_16765, YR17_10960, YT65_22010, Z700_22650, Z705_18140, ZB89_19920, ZC54_19680, ZT09_16805, ZT28_13365, ZT74_18075, ZT89_18160, ZU86_17815, ZU92_16805, ZV06_14780, ZV17_16185, ZV33_17250, ZV34_18355, ZV38_13400, ZV58_19590, ZV70_18315, ZV76_14470, ZV78_21800, ZV90_21250, ZW74_16110, ZX03_15750, ZY23_11835, ZY27_17660, ZY40_02770, ZY51_16230, ZZ18_15945, ZZ43_13745, ZZ77_13130, ZZ79_15595 Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 4000, Tris-HCl pH 8.5, 0.2M MgCl2 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→28.71 Å / Num. obs: 7616 / % possible obs: 97 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.079 / Net I/σ(I): 16.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5O8Z Resolution: 2.5→28.71 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.864 / SU B: 12.988 / SU ML: 0.289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.67 Å2 / Biso mean: 31.525 Å2 / Biso min: 13.23 Å2
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Refinement step | Cycle: final / Resolution: 2.5→28.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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