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Yorodumi- PDB-1d8h: X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WI... -
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-Basic information
Entry | Database: PDB / ID: 1d8h | ||||||
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Title | X-RAY CRYSTAL STRUCTURE OF YEAST RNA TRIPHOSPHATASE IN COMPLEX WITH SULFATE AND MANGANESE IONS. | ||||||
Components | mRNA TRIPHOSPHATASE CET1 | ||||||
Keywords | HYDROLASE / RNA TRIPHOSPHATASE / BETA SUBUNIT / POLYNUCLEOTIDE 5'-TRIPHOSPHATASE / mRNA PROCESSING / mRNA CAPPING / NUCLEAR PROTEIN BETA BARREL / CATALYTIC DOMAIN / DIMER / MANGANESE-SULFATE COMPLEX | ||||||
Function / homology | Function and homology information mRNA capping enzyme complex / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / 7-methylguanosine mRNA capping / positive regulation of transcription elongation by RNA polymerase II / positive regulation of protein localization to nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Lima, C.D. / Wang, L.K. / Shuman, S. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1999 Title: Structure and mechanism of yeast RNA triphosphatase: an essential component of the mRNA capping apparatus. Authors: Lima, C.D. / Wang, L.K. / Shuman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d8h.cif.gz | 212.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d8h.ent.gz | 161.7 KB | Display | PDB format |
PDBx/mmJSON format | 1d8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1d8h_validation.pdf.gz | 411.4 KB | Display | wwPDB validaton report |
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Full document | 1d8h_full_validation.pdf.gz | 536.3 KB | Display | |
Data in XML | 1d8h_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 1d8h_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d8/1d8h ftp://data.pdbj.org/pub/pdb/validation_reports/d8/1d8h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35691.465 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid details: T7 PROMOTER / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O13297, polynucleotide 5'-phosphatase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | RNA triphosphatase is an essential mRNA processing enzyme that catalyzes the first step in 5' cap ...RNA triphosphatase is an essential mRNA processing enzyme that catalyzes the first step in 5' cap formation. The 2.05 A crystal structure of yeast RNA triphosphatase Cet1p reveals a novel active site fold whereby an 8-strand beta barrel forms a topologically closed triphosphatase tunnel. Interactions of a sulfate bound in the center of the tunnel with a divalent cation and basic amino acids projecting into the tunnel suggest a catalytic mechanism that is supported by mutational data. Discrete surface domains are responsible for Cet1p homodimerization and Cet1p-binding to the guanylyltransferase component of the yeast capping apparatus. The structure and mechanism of the fungal RNA triphosphatases are completely different from those of the mammalian mRNA capping enzymes. | Sequence details | THE EXPRESSION CONSTRUCTS USED TO PRODUCE THE RECOMBINANT PROTEIN INCLUDED AN N-TERMINAL HIS TAG ...THE EXPRESSION | |
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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: 2.61 Å3/Da / Density % sol: 52.9 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.34 Details: 0.1M MES, 38% SATURATED (NH4)2SO4, 5MM DTT STABILIZED IN 2.5M AMSO4 + BUFFER, 200MM MNCL2 IN STABILIZATION CONDITION FOR MANGANESE COMPLEX, pH 6.34, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃Details: drop solution was mixed with an equal volume of reservoir solution | |||||||||||||||||||||||||
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: NSLS / Beamline: X4A / Wavelength: 1.2141 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 8, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2141 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 72277 / Num. obs: 63710 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 22.199 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.261 / % possible all: 72.2 |
Reflection shell | *PLUS % possible obs: 72.2 % |
-Processing
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Refinement | Resolution: 2→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: RESTRAINED MAXIMUM LIKELIHOOD FOR FS CONJUGATE DIRECTION EXPERIMENTAL SIGMAS USED FOR WEIGHTING
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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