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Yorodumi- PDB-3q24: X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3q24 | ||||||
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Title | X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation complex with pppGpG and pyrophosphate: product complex | ||||||
Components |
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Keywords | TRANSFERASE/DNA/RNA / PROTEIN-DNA COMPLEX / TWO-METAL CATALYSIS / DE NOVO TRANSCRIPTION INITIATION / NUCLEOTIDYLTRANSFERASE / INITIATION COMPLEX / DNA-HAIRPIN / VIRION RNA POLYMERASE / TRANSFERASE-DNA-RNA COMPLEX | ||||||
Function / homology | Function and homology information DNA-directed RNA polymerase complex / virion component / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / GTP binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage N4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Gleghorn, M.L. / Murakami, K.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: X-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides. Authors: Gleghorn, M.L. / Davydova, E.K. / Basu, R. / Rothman-Denes, L.B. / Murakami, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3q24.cif.gz | 519 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q24.ent.gz | 406.6 KB | Display | PDB format |
PDBx/mmJSON format | 3q24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/3q24 ftp://data.pdbj.org/pub/pdb/validation_reports/q2/3q24 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein / DNA chain , 2 types, 4 molecules ABCD
#1: Protein | Mass: 123036.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage N4 (virus) / Gene: gp50 / Plasmid: PKMK56 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q859P9, DNA-directed RNA polymerase #2: DNA chain | Mass: 11007.082 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 5 types, 2405 molecules
#3: Chemical | ChemComp-GTP / | ||||
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#4: Chemical | ChemComp-G / | ||||
#5: Chemical | #6: Chemical | #7: 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: 2.41 Å3/Da / Density % sol: 48.96 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: hanging drop / pH: 8 Details: 0.1 M TRIS-HCL, 0.21 M DIBASIC AMMONIUM CITRATE, 0.09 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, 25% (DROP) 21.5-22% (RESERVOIR) PEG 3350, pH 8.0, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.959997 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2006 |
Radiation | Monochromator: Silicon(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.959997 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 233493 / Num. obs: 233493 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.728 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→41.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.791 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→41.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.86 Å / Total num. of bins used: 20
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