+Open data
-Basic information
Entry | Database: PDB / ID: 1jpj | ||||||
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Title | GMPPNP Complex of SRP GTPase NG Domain | ||||||
Components | SIGNAL RECOGNITION PARTICLE PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / Ffh / SRP / GMPPNP / SIGNAL RECOGNITION PARTICLE / SRP54 / NG DOMAIN | ||||||
Function / homology | Function and homology information signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity Similarity search - Function | ||||||
Biological species | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Padmanabhan, S. / Freymann, D.M. | ||||||
Citation | Journal: Structure / Year: 2001 Title: The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase. Authors: Padmanabhan, S. / Freymann, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jpj.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jpj.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jp/1jpj ftp://data.pdbj.org/pub/pdb/validation_reports/jp/1jpj | HTTPS FTP |
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-Related structure data
Related structure data | 1jpnC 1ffhS 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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Unit cell |
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-Components
#1: Protein | Mass: 32472.508 Da / Num. of mol.: 1 / Fragment: NG domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: pET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O07347 |
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#2: Chemical | ChemComp-GNP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.65 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 10% PEG 1000, 10% PEG 6000, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
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: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 12838 / Num. obs: 10955 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.171 / Rsym value: 0.171 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ffh Resolution: 2.3→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.5 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 8 % / Rfactor obs: 0.203 / Rfactor Rfree: 0.299 / Rfactor Rwork: 0.203 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.5 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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