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Yorodumi- PDB-1uvk: The structural basis for RNA specificity and Ca2 inhibition of an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uvk | ||||||
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Title | The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complex | ||||||
Components | RNA-directed RNA polymeraseRNA-dependent RNA polymerase | ||||||
Keywords | TRANSFERASE / POLYMERASE-COMPLEX / OLIGONUCLEOTIDE / POLYMERASE | ||||||
Function / homology | Function and homology information RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas phage phi6 (bacteriophage) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Salgado, P.S. / Makeyev, E.V. / Butcher, S. / Bamford, D. / Stuart, D.I. / Grimes, J.M. | ||||||
Citation | Journal: Structure / Year: 2004 Title: The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase. Authors: Salgado, P.S. / Makeyev, E.V. / Butcher, S.J. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uvk.cif.gz | 405 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uvk.ent.gz | 329.2 KB | Display | PDB format |
PDBx/mmJSON format | 1uvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/1uvk ftp://data.pdbj.org/pub/pdb/validation_reports/uv/1uvk | HTTPS FTP |
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-Related structure data
Related structure data | 1uviC 1uvjC 1uvlC 1uvmC 1uvnC 1hhsS 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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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE POLYMERASE IS A MONOMER IN SOLUTION, BUT SINCE IT IS IN COMPLEX WITH RNA IN THIS ENTRY, THE OLIGOMER IS ANNOTATED AS A DIMER |
-Components
-Protein , 1 types, 3 molecules ACE
#1: Protein | Mass: 74903.203 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage phi6 (bacteriophage) / Gene: P2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11124, RNA-directed RNA polymerase |
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-Non-polymers , 6 types, 279 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | FUNCTION: P2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID, WHICH IS RESPONSIBLE ...FUNCTION: P2 IS ONE OF THE 4 STRUCTURAL |
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Sequence details | THE PROTEIN WAS CO-CRYSTALLIZED WITH A 5NT RNA SEQUENCE 5-U-U-U-C-C-3. HOWEVER, NO TRACE OF RNA WAS ...THE PROTEIN WAS CO-CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.4 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.3 Details: 100MM HEPES PH7.3, 13% PEG 20000, 2MM MNCL2, 2% EG, 0.036MG PROTEIN INCUBATED WITH 0.006MM 5NT RNA SOAKING: 25MM MGCL2, 40-60MM GTP, pH 7.30 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 6.7 / Method: vapor diffusion, sitting dropDetails: Butcher, S.J., (2000) Acta Crystallogr.,Sect.D, D56, 1473. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.542 |
Detector | Date: Nov 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 97099 / % possible obs: 97.7 % / Observed criterion σ(I): 3.3 / Redundancy: 48 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 3.4 / % possible all: 96.1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. obs: 97851 / Num. measured all: 4701397 / Rmerge(I) obs: 0.136 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 96 % / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HHS Resolution: 2.45→19.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2002882.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED DISORDERED LOOP: R607-E613. PROTEIN WAS CO-CRYSTALLIZED WITH A 5NT RNA OLIGO AND SOAKED WITH GTP. CATALYSIS OCCURED IN THE CRYSTAL AND THE GTP HYDROLYSIS PRODUCT ...Details: BULK SOLVENT MODEL USED DISORDERED LOOP: R607-E613. PROTEIN WAS CO-CRYSTALLIZED WITH A 5NT RNA OLIGO AND SOAKED WITH GTP. CATALYSIS OCCURED IN THE CRYSTAL AND THE GTP HYDROLYSIS PRODUCT GUANYLYL(3'-5') -GUANOSINE-5'- TRIPHOSPHATE (GPGPPP) AND THE BYPRODUCT PPI WERE DETECTED IN ED MAPS. NO RNA WAS TRACEABLE. S SITE 3'CYT RECOGNITION POCKET: LOOP: Y630-K631-W632 SUBSTRATE/BYPRODUCTS PORE: R225, R268,R270
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32 Å2 / ksol: 0.343709 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.45→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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