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- PDB-6tyg: Crystal structure of MTB sigma L transcription initiation complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tyg | ||||||
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Title | Crystal structure of MTB sigma L transcription initiation complex with 9 nt long RNA primer | ||||||
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Function / homology | ![]() Antimicrobial action and antimicrobial resistance in Mtb / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Molodtsov, V. / Ebright, R.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription. Authors: Li, L. / Molodtsov, V. / Lin, W. / Ebright, R.H. / Zhang, Y. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / ![]() Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2.1 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6konC ![]() 6kooC ![]() 6kopC ![]() 6koqC ![]() 6kqdC ![]() 6kqeC ![]() 6kqfC ![]() 6kqgC ![]() 6kqhC ![]() 6kqlC ![]() 6kqmC ![]() 6kqnC ![]() 6l74C ![]() 6ltsC ![]() 6tyeC ![]() 6tyfC ![]() 6dvcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2 - 225 / Label seq-ID: 2 - 225
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Components
-DNA chain , 2 types, 2 molecules GH
#2: DNA chain | Mass: 6215.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
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#3: DNA chain | Mass: 8373.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#5: Protein | ![]() Mass: 37745.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: A5U8D3, UniProt: P9WGZ1*PLUS, ![]() #6: Protein | | ![]() Mass: 130018.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P9WGY8, UniProt: P9WGY9*PLUS, ![]() #7: Protein | | ![]() Mass: 146968.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: rpoC, rpoC_1, rpoC_2, DKC2_0716, ERS007665_00591, ERS023446_00410, ERS031537_00289, ERS124361_01694, EUB02_01475, EUB03_00860, EUB11_05575, SAMEA2682835_07420, SAMEA2682864_01702 Production host: ![]() ![]() ![]() References: UniProt: A0A045J9E2, UniProt: P9WGY7*PLUS, ![]() #8: Protein | | ![]() Mass: 11851.140 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: rpoZ, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445, ERS007722_03066, ERS007741_03196, ERS023446_ ...Gene: rpoZ, DKC2_1480, DSI35_24025, ERS007657_03145, ERS007661_02963, ERS007663_02972, ERS007665_03743, ERS007670_03615, ERS007679_02942, ERS007681_04445, ERS007722_03066, ERS007741_03196, ERS023446_03677, ERS024213_01369, ERS024276_01577, ERS027644_00478, ERS027646_01439, ERS027651_03169, ERS027653_00843, ERS027659_01429, ERS027661_02200, ERS027666_04715, ERS031537_03443, EU767_08910, EU768_15085, EU769_05250, EU770_14555, EU771_05130, EU773_14340, EU774_06465, EU775_07590, EU776_17830, EU777_06800, EUB02_12495, EUB03_09550, EUB06_03645, EUB07_12165, EUB08_05285, EUB09_00425, EUB10_04215, EUB11_10790, EUB13_01060, EUB14_01055, EUB16_00425, SAMEA2682864_01599, SAMEA2683035_01133 Production host: ![]() ![]() ![]() References: UniProt: A0A045H2R3, UniProt: P9WGY5*PLUS, ![]() |
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-Protein / RNA chain , 2 types, 2 molecules FI
#1: Protein | Mass: 19563.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: sigL, sigX, DKC2_0784, DSI35_13315, ERS007657_01744, ERS007661_01946, ERS007670_03245, ERS007672_04865, ERS007688_03724, ERS007722_03570, ERS007731_02151, ERS007741_04102, ERS023446_03871, ...Gene: sigL, sigX, DKC2_0784, DSI35_13315, ERS007657_01744, ERS007661_01946, ERS007670_03245, ERS007672_04865, ERS007688_03724, ERS007722_03570, ERS007731_02151, ERS007741_04102, ERS023446_03871, ERS024213_03781, ERS027644_01708, ERS027646_03649, ERS027651_00554, ERS027654_02031, ERS027659_03608, ERS027661_02428, ERS027666_03497, ERS031537_01383, ERS124361_02832, EU767_20440, EU768_17405, EU769_19535, EU770_10565, EU771_18640, EU773_15915, EU774_01235, EU775_01235, EU776_08285, EU777_18775, EUB02_13395, EUB03_01225, EUB07_01225, EUB08_01615, EUB09_12390, EUB10_16580, EUB11_05940, EUB12_18145, EUB13_14065, EUB14_03980, EUB16_03020, SAMEA2682835_06130, SAMEA2682864_01771, SAMEA2683035_02456 Production host: ![]() ![]() ![]() |
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#4: RNA chain | Mass: 2790.735 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium citrate tribasic dihydrate, pH 5.6, 200 mM sodium acetate, and 10% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.41→49.64 Å / Num. obs: 55779 / % possible obs: 99 % / Redundancy: 6.8 % / Biso Wilson estimate: 84.64 Å2 / CC1/2: 0.976 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 3.41→3.68 Å / Num. unique obs: 11415 / CC1/2: 0.976 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6DVC Resolution: 3.5→49.64 Å / SU ML: 0.4319 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1426 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 109.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→49.64 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 3.26878342827 Å / Origin y: -7.73906052926 Å / Origin z: -15.5405548074 Å
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Refinement TLS group | Selection details: all |