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Yorodumi- PDB-1j3l: Structure of the RNA-processing inhibitor RraA from Thermus therm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j3l | ||||||
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Title | Structure of the RNA-processing inhibitor RraA from Thermus thermophilis | ||||||
Components | Demethylmenaquinone Methyltransferase | ||||||
Keywords | TRANSFERASE / Vitamine K2 / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information 4-hydroxy-4-methyl-2-oxoglutarate aldolase / 4-hydroxy-4-methyl-2-oxoglutarate aldolase activity / oxaloacetate decarboxylase / ribonuclease inhibitor activity / regulation of RNA metabolic process / oxaloacetate decarboxylase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Rehse, P.H. / Miyano, M. / Tahirov, T.H. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure of the RNA-processing inhibitor RraA from Thermus thermophilis. Authors: Rehse, P.H. / Kuroishi, C. / Tahirov, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j3l.cif.gz | 198.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j3l.ent.gz | 159.3 KB | Display | PDB format |
PDBx/mmJSON format | 1j3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j3l_validation.pdf.gz | 478.8 KB | Display | wwPDB validaton report |
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Full document | 1j3l_full_validation.pdf.gz | 512.8 KB | Display | |
Data in XML | 1j3l_validation.xml.gz | 43.3 KB | Display | |
Data in CIF | 1j3l_validation.cif.gz | 60.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j3l ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j3l | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-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 on special symmetry positions |
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Details | The biological assembly is a trimer, two of which are in the assymetric unit. Trimer 1 is made up of Chains A,B and C, Trimer 2 is made up of chains D, E and F. |
-Components
#1: Protein | Mass: 17456.850 Da / Num. of mol.: 6 / Mutation: L80R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HD8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) References: UniProt: P83846, UniProt: Q5SIP7*PLUS, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-MG / | #3: Chemical | #4: 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: 2.12 Å3/Da / Density % sol: 41.46 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: PEG 1000, magnesium chloride, Tris-Cl, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 296K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, sitting 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: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97900, 0.97925, 0.97000 | ||||||||||||
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 9, 2002 | ||||||||||||
Radiation | Monochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→38.5 Å / Num. all: 193179 / Num. obs: 191090 / % possible obs: 98.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.05 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 15.96 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 3.32 / Num. unique all: 3762 / % possible all: 92.3 | ||||||||||||
Reflection | *PLUS % possible obs: 90.8 % / Redundancy: 5.1 % | ||||||||||||
Reflection shell | *PLUS % possible obs: 92.3 % / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→38.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 231118.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The following residues have been built into weak density and therefore should be interpretted with caution: A1, B160-164, C159-161, D158-163, E158-161 and F154:157
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.209 Å2 / ksol: 0.29942 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→38.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 38.5 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.217 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.323 |