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Yorodumi- PDB-1j8m: Signal Recognition Particle conserved GTPase domain from A. ambivalens -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j8m | ||||||
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Title | Signal Recognition Particle conserved GTPase domain from A. ambivalens | ||||||
Components | SIGNAL RECOGNITION 54 KDA PROTEIN | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol Similarity search - Function | ||||||
Biological species | Acidianus ambivalens (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Montoya, G. / te Kaat, K. / Moll, R. / Schafer, G. / Sinning, I. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: The crystal structure of the conserved GTPase of SRP54 from the archaeon Acidianus ambivalens and its comparison with related structures suggests a model for the SRP-SRP receptor complex. Authors: Montoya, G. / Kaat, K. / Moll, R. / Schafer, G. / Sinning, I. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and Preliminary X-ray Diffraction Studies on the Conserved GTPase Domain of the Signal Recognition Particle from Acidianus ambivalens Authors: Montoya, G. / te Kaat, K. / Moll, R. / Schafer, G. / Sinning, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j8m.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j8m.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 1j8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j8m_validation.pdf.gz | 368.3 KB | Display | wwPDB validaton report |
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Full document | 1j8m_full_validation.pdf.gz | 379.9 KB | Display | |
Data in XML | 1j8m_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 1j8m_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/1j8m ftp://data.pdbj.org/pub/pdb/validation_reports/j8/1j8m | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32839.918 Da / Num. of mol.: 1 / Fragment: G-DOMAIN, GTPASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidianus ambivalens (archaea) / Plasmid: pET-16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P70722 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.94 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.932 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 20842 |
Reflection | *PLUS Observed criterion σ(I): 0 / Num. measured all: 451808 / Rmerge(I) obs: 0.051 |
-Processing
Software |
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Refinement | Resolution: 2→25 Å / SU B: 5.058 / SU ML: 0.145 / SU Rfree: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.196
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Displacement parameters | Biso mean: 22.511 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20 /
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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