+Open data
-Basic information
Entry | Database: PDB / ID: 5y7m | ||||||
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Title | Crystal structure of PhoRpp38 bound to a K-turn in P12.1 helix | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / Kink-turn RNA / Ribonuclease P | ||||||
Function / homology | Function and homology information ribonuclease P activity / tRNA 5'-leader removal / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) Pyrococcus horikoshii OT3 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | ||||||
Authors | Oshima, K. / Kimura, M. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif. Authors: Oshima, K. / Gao, X. / Hayashi, S. / Ueda, T. / Nakashima, T. / Kimura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y7m.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y7m.ent.gz | 89.1 KB | Display | PDB format |
PDBx/mmJSON format | 5y7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/5y7m ftp://data.pdbj.org/pub/pdb/validation_reports/y7/5y7m | HTTPS FTP |
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-Related structure data
Related structure data | 5xtmC 2czwS C: citing same article (ref.) S: Starting model for refinement |
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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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Unit cell |
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-Components
#1: Protein | Mass: 14645.026 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: rpl7ae, PH1496 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62009 #2: RNA chain | Mass: 16552.934 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Pyrococcus horikoshii OT3 (archaea) #3: Chemical | #4: Chemical | ChemComp-SO4 / |
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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: 4.56 Å3/Da / Density % sol: 73.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: sodium cacodylate ammonium solfate magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 3, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→48.376 Å / Num. obs: 20596 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.801 % / Biso Wilson estimate: 57.25 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.197 / Rrim(I) all: 0.229 / Χ2: 0.939 / Net I/σ(I): 7.05 / Num. measured all: 78285 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2czw Resolution: 3.1→48.376 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 223.77 Å2 / Biso mean: 72.6709 Å2 / Biso min: 36.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→48.376 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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