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Yorodumi- PDB-1ng1: N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ng1 | ||||||
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Title | N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN FFH FROM THERMUS AQUATICUS | ||||||
Components | SIGNAL SEQUENCE RECOGNITION PROTEIN FFH | ||||||
Keywords | SIGNAL RECOGNITION / FFH / SRP / GTPASE / SIGNAL RECOGNITION PARTICLE / GDP / MG | ||||||
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: 2.03 Å | ||||||
Authors | Freymann, D.M. / Stroud, R.M. / Walter, P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: Functional changes in the structure of the SRP GTPase on binding GDP and Mg2+GDP. Authors: Freymann, D.M. / Keenan, R.J. / Stroud, R.M. / Walter, P. #1: Journal: Nature / Year: 1997 Title: Structure of the Conserved Gtpase Domain of the Signal Recognition Particle Authors: Freymann, D.M. / Keenan, R.J. / Stroud, R.M. / Walter, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ng1.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ng1.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ng1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/1ng1 ftp://data.pdbj.org/pub/pdb/validation_reports/ng/1ng1 | HTTPS FTP |
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-Related structure data
Related structure data | 2ng1C 3ng1C 1ffhS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32300.371 Da / Num. of mol.: 1 / Fragment: NG GTPASE FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Gene: FFH / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSE / References: UniProt: O07347 |
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-Non-polymers , 6 types, 188 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GDP / | #5: Chemical | #6: Chemical | ChemComp-ACY / #7: 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: 2.85 Å3/Da / Density % sol: 57 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 4, 1997 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→20 Å / Num. obs: 24684 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 2.03→2.1 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.396 / % possible all: 100 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FFH Resolution: 2.03→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 Details: A BULK SOLVENT CORRECTION, AS IMPLEMENTED IN X-PLOR 3.843 WAS APPLIED DURING THE REFINEMENT.
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Displacement parameters | Biso mean: 25.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.09 Å / Total num. of bins used: 12
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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