[English] 日本語
Yorodumi- PDB-5uha: Crystal structure of Mycobacterium tuberculosis transcription ini... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uha | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis transcription initiation complex | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION/DNA / RNA polymerase complex / transcription / DNA / RNA / TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information response to water / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity ...response to water / Antimicrobial action and antimicrobial resistance in Mtb / sigma factor activity / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / response to antibiotic / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.906 Å | ||||||
Authors | Lin, W. / Das, K. / Feng, Y. / Ebright, R.H. | ||||||
Citation | Journal: Mol. Cell / Year: 2017 Title: Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition. Authors: Lin, W. / Mandal, S. / Degen, D. / Liu, Y. / Ebright, Y.W. / Li, S. / Feng, Y. / Zhang, Y. / Mandal, S. / Jiang, Y. / Liu, S. / Gigliotti, M. / Talaue, M. / Connell, N. / Das, K. / Arnold, E. / Ebright, R.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5uha.cif.gz | 669.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5uha.ent.gz | 526.8 KB | Display | PDB format |
PDBx/mmJSON format | 5uha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uha_validation.pdf.gz | 501.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5uha_full_validation.pdf.gz | 544 KB | Display | |
Data in XML | 5uha_validation.xml.gz | 107.7 KB | Display | |
Data in CIF | 5uha_validation.cif.gz | 146.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/5uha ftp://data.pdbj.org/pub/pdb/validation_reports/uh/5uha | HTTPS FTP |
-Related structure data
Related structure data | 5uh5C 5uh6C 5uh7C 5uh8C 5uh9C 5uhbC 5uhcC 5uhdC 5uheC 5uhfC 5uhgC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 37745.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoA, Rv3457c, MTCY13E12.10c Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WGZ1, DNA-directed RNA polymerase #2: Protein | | Mass: 130018.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoB, Rv0667, MTCI376.08c Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WGY9, DNA-directed RNA polymerase #3: Protein | | Mass: 146968.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoC, Rv0668, MTCI376.07c Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WGY7, DNA-directed RNA polymerase #4: Protein | | Mass: 11851.140 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: rpoZ, Rv1390, MTCY21B4.07 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WGY5, DNA-directed RNA polymerase |
---|
-Protein , 1 types, 1 molecules F
#5: Protein | Mass: 57877.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: sigA, mysA, rpoD, rpoV, Rv2703, MTCY05A6.24 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P9WGI1 |
---|
-DNA chain , 2 types, 2 molecules HG
#6: DNA chain | Mass: 7160.632 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) |
---|---|
#7: DNA chain | Mass: 4939.204 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) |
-Non-polymers , 2 types, 3 molecules
#8: Chemical | #9: Chemical | ChemComp-MG / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.32 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: 50 mM Tris-HCl, pH 8.2, 200 mM KCl, 50 mM MgCl2, and 10% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.925 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 9, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.925 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.9→50 Å / Num. obs: 44080 / % possible obs: 99.2 % / Redundancy: 15 % / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.057 / Rrim(I) all: 0.226 / Χ2: 0.975 / Net I/σ(I): 3.6 / Num. measured all: 659212 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 3.906→48.913 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 21.28 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso max: 179.92 Å2 / Biso mean: 38.2255 Å2 / Biso min: 0.01 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.906→48.913 Å
|