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Yorodumi- PDB-4kbm: Structure of the Mtb CarD/RNAP Beta subunit B1-B2 domains complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kbm | ||||||
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Title | Structure of the Mtb CarD/RNAP Beta subunit B1-B2 domains complex | ||||||
Components |
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Keywords | TRANSFERASE/TRANSCRIPTION / Structural Genomics / TB Structural Genomics Consortium / TBSGC / Tudor / DNA-dependent RNA polymerase / transcription regulator / protein-protein complex / CarD / DNA / sigma factor / TRANSFERASE-TRANSCRIPTION complex | ||||||
Function / homology | Function and homology information regulation of growth rate / Antimicrobial action and antimicrobial resistance in Mtb / cell wall / stringent response / rRNA transcription / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...regulation of growth rate / Antimicrobial action and antimicrobial resistance in Mtb / cell wall / stringent response / rRNA transcription / DNA-directed RNA polymerase complex / peptidoglycan-based cell wall / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to antibiotic / DNA-templated transcription / DNA binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1146 Å | ||||||
Authors | Gulten, G. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Structure / Year: 2013 Title: Structure of the Mtb CarD/RNAP beta-Lobes Complex Reveals the Molecular Basis of Interaction and Presents a Distinct DNA-Binding Domain for Mtb CarD. Authors: Gulten, G. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kbm.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kbm.ent.gz | 173.4 KB | Display | PDB format |
PDBx/mmJSON format | 4kbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/4kbm ftp://data.pdbj.org/pub/pdb/validation_reports/kb/4kbm | HTTPS FTP |
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-Related structure data
Related structure data | 4kbjSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46266.324 Da / Num. of mol.: 1 / Fragment: B1 and B2 domains of Mtb RNAP Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0695, MTCI376.08c, rpoB, Rv0667 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS References: UniProt: P0A680, UniProt: P9WGY9*PLUS, DNA-directed RNA polymerase |
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#2: Protein | Mass: 17933.361 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: carD, MT3689, Rv3583c / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: O53568, UniProt: P9WJG3*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 14% PEG 3350, 2% tacsimate pH 5.0, 0.1 M sodium citrate tribasic dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å |
Detector | Type: MAR 300 / Detector: CCD / Date: Jun 9, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→37.59 Å / Num. all: 40844 / Num. obs: 40844 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.11→2.21 Å / Mean I/σ(I) obs: 2.03 / Num. unique all: 4675 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4KBJ Resolution: 2.1146→37.588 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.559 Å2 / ksol: 0.321 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1146→37.588 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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