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Yorodumi- PDB-1go3: Structure of an archeal homolog of the eukaryotic RNA polymerase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1go3 | ||||||
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Title | Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex | ||||||
Components |
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Keywords | TRANSFERASE / TRANSCRIPTION / DNA-DIRECTED RNA POLYMERASE | ||||||
Function / homology | Function and homology information RNA polymerase complex / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / nucleotide binding / DNA-templated transcription / DNA binding Similarity search - Function | ||||||
Biological species | METHANOCOCCUS JANNASCHII (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.75 Å | ||||||
Authors | Todone, F. / Brick, P. / Werner, F. / Weinzierl, R.O.J. / Onesti, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Structure of an Archaeal Homolog of the Eukaryotic RNA Polymerase II Rpb4/Rpb7 Complex Authors: Todone, F. / Brick, P. / Werner, F. / Weinzierl, R.O.J. / Onesti, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EB" AND "MB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EB" AND "MB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1go3.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1go3.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 1go3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/1go3 ftp://data.pdbj.org/pub/pdb/validation_reports/go/1go3 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.12195, -0.99217, 0.02686), Vector: |
-Components
#1: Protein | Mass: 21246.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOCOCCUS JANNASCHII (archaea) Description: CO-EXPRESSED USING A BICISTRIONIC EXPRESSION STRATEGY Plasmid: PGEX-2TK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57840, DNA-directed RNA polymerase #2: Protein | Mass: 12342.216 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) METHANOCOCCUS JANNASCHII (archaea) Description: CO-EXPRESSED USING A BICISTRIONIC EXPRESSION STRATEGY Plasmid: PGEX-2TX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q60351, DNA-directed RNA polymerase #3: 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: 2.9 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: 100 MM TRIS/ HCL 1.3-1.4 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, pH 4.60 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1 |
Detector | Detector: CCD / Date: Feb 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→27.8 Å / Num. obs: 76814 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 28 Å |
Reflection shell | *PLUS % possible obs: 99.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.75→27.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2534087 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODE / Bsol: 60.16 Å2 / ksol: 0.39 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→27.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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