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Yorodumi- PDB-4xlr: Crystal structure of T.aquaticus transcription initiation complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xlr | ||||||
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Title | Crystal structure of T.aquaticus transcription initiation complex with CarD containing bubble promoter and RNA | ||||||
Components |
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Keywords | transcription/DNA / protein-DNA complex / Bacterial transcription initiation complex / transcription-DNA complex | ||||||
Function / homology | Function and homology information sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding ...sigma factor activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) Thermus thermophilus JL-18 (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.3 Å | ||||||
Authors | Bae, B. / Darst, S.A. | ||||||
Citation | Journal: Elife / Year: 2015 Title: CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex. Authors: Bae, B. / Chen, J. / Davis, E. / Leon, K. / Darst, S.A. / Campbell, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xlr.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4xlr.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 4xlr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/4xlr ftp://data.pdbj.org/pub/pdb/validation_reports/xl/4xlr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABGHCIDJEK
#1: Protein | Mass: 34830.895 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU8, DNA-directed RNA polymerase #2: Protein | Mass: 124930.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU7, DNA-directed RNA polymerase #3: Protein | Mass: 171187.516 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9KWU6, DNA-directed RNA polymerase #4: Protein | Mass: 11642.423 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Thermus aquaticus (bacteria) / References: UniProt: Q9EVV4, DNA-directed RNA polymerase |
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-Protein , 2 types, 4 molecules FLMN
#5: Protein | Mass: 39864.730 Da / Num. of mol.: 2 / Fragment: unp residues 92-438 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: sigA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9EZJ8 #6: Protein | Mass: 18316.014 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus JL-18 (bacteria) / Gene: TtJL18_0238 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H9ZP94 |
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-DNA chain , 2 types, 4 molecules ORPS
#7: DNA chain | Mass: 14878.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA non-template strand / Source: (synth.) synthetic construct (others) #8: DNA chain | Mass: 14831.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA template strand / Source: (synth.) synthetic construct (others) |
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-RNA chain , 1 types, 2 molecules QT
#9: RNA chain | Mass: 1240.802 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA transcript / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 2 types, 6 molecules
#10: Chemical | ChemComp-ZN / #11: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.03 Å3/Da / Density % sol: 79.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: ammonium sulfate, magnesium chloride, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.15→40 Å / Num. obs: 171617 / % possible obs: 97.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 165.1 Å2 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.137 / Rrim(I) all: 0.222 / Χ2: 1.869 / Net I/av σ(I): 3.314 / Net I/σ(I): 2 / Num. measured all: 1302221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.3→39.562 Å / SU ML: 1.01 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.3→39.562 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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