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Yorodumi- PDB-5d4d: Crystal structure of Thermus thermophilus product complex for tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d4d | ||||||
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Title | Crystal structure of Thermus thermophilus product complex for transcription initiation with NAD and CTP | ||||||
Components |
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Keywords | transcription/dna / RNA polymerase / transcription initiation / bacterial / NCIN / non-canonical initiating nucleotide / primer-dependent initiation / DNA / Single-Stranded / DNA-Directed RNA Polymerases / Gene Expression Regulation / Promoter Regions / Genetic / Protein Conformation / Sigma Factor / 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 / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Zhang, Y. / Ebright, R.H. | ||||||
Citation | Journal: Nature / Year: 2016 Title: The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA. Authors: Bird, J.G. / Zhang, Y. / Tian, Y. / Panova, N. / Barvik, I. / Greene, L. / Liu, M. / Buckley, B. / Krasny, L. / Lee, J.K. / Kaplan, C.D. / Ebright, R.H. / Nickels, B.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d4d.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5d4d.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5d4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/5d4d ftp://data.pdbj.org/pub/pdb/validation_reports/d4/5d4d | HTTPS FTP |
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-Related structure data
Related structure data | 5d4cC 5d4eC 4g7hS 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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2 |
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Unit cell |
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-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 10 molecules ABKLCMDNEO
#1: Protein | Mass: 35056.164 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) References: UniProt: Q9Z9H6, UniProt: Q5SHR6*PLUS, DNA-directed RNA polymerase #2: Protein | Mass: 125436.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE9, DNA-directed RNA polymerase #3: Protein | Mass: 170997.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE8, DNA-directed RNA polymerase #4: Protein | Mass: 11533.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q8RQE7, DNA-directed RNA polymerase |
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-Protein , 1 types, 2 molecules FP
#5: Protein | Mass: 50769.398 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (bacteria) Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: sigA, rpoD, TT_C0164 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72L95, UniProt: Q5SKW1*PLUS |
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-DNA chain , 2 types, 4 molecules GRHS
#6: DNA chain | Mass: 5845.786 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) #7: DNA chain | Mass: 8421.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
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-Non-polymers , 7 types, 915 molecules
#8: Chemical | ChemComp-MG / #9: Chemical | ChemComp-ZN / #10: Chemical | #11: Chemical | #12: Chemical | ChemComp-NAD / | #13: Chemical | ChemComp-A / | #14: Water | ChemComp-HOH / | |
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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: 3.17 Å3/Da / Density % sol: 61.17 % / Description: rod |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 100 mM Tris-HCl, pH 8.4, 200 mM potassium chloride, 50 mM magnesium chloride, 9.5% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 219058 / % possible obs: 97.9 % / Redundancy: 4 % / Biso Wilson estimate: 48.75 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.067 / Rrim(I) all: 0.132 / Rsym value: 0.119 / Χ2: 1.095 / Net I/av σ(I): 10.571 / Net I/σ(I): 7.2 / Num. measured all: 869839 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G7H Resolution: 3→42.173 Å / FOM work R set: 0.8048 / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.59 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 170.1 Å2 / Biso mean: 31.84 Å2 / Biso min: 0.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→42.173 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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