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Yorodumi- PDB-5d4c: Crystal structure of Thermus thermophilus product complex for tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d4c | |||||||||
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Title | Crystal structure of Thermus thermophilus product complex for transcription initiation with ATP 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 / Thermus thermophilus / TRANSCRIPTION / 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: 3.28 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 | 5d4c.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5d4c.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5d4c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d4c_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 5d4c_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5d4c_validation.xml.gz | 226.2 KB | Display | |
Data in CIF | 5d4c_validation.cif.gz | 306.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/5d4c ftp://data.pdbj.org/pub/pdb/validation_reports/d4/5d4c | HTTPS FTP |
-Related structure data
Related structure data | 5d4dC 5d4eC 4h7hS C: citing same article (ref.) S: Starting model for refinement |
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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 HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: sigA, TTHA0532 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SKW1 |
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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 , 6 types, 79 molecules
#8: Chemical | ChemComp-MG / #9: Chemical | ChemComp-ZN / #10: Chemical | #11: Chemical | #12: Chemical | #13: 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: 3.22 Å3/Da / Density % sol: 61.76 % / 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: NSLS / Beamline: X29A / Wavelength: 1.075 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→50 Å / Num. all: 892176 / Num. obs: 164255 / % possible obs: 96.1 % / Redundancy: 5.4 % / Biso Wilson estimate: 57.72 Å2 / Rmerge(I) obs: 0.185 / Rpim(I) all: 0.084 / Rrim(I) all: 0.197 / Rsym value: 0.185 / Χ2: 1.112 / Net I/av σ(I): 8.672 / Net I/σ(I): 5.6 / Num. measured all: 892176 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4H7H Resolution: 3.28→49.196 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 27.54 / 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: 3.28→49.196 Å
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Refine LS restraints |
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LS refinement shell |
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