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- PDB-2ng1: N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN F... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ng1 | ||||||
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Title | N AND GTPASE DOMAINS OF THE SIGNAL SEQUENCE RECOGNITION PROTEIN FFH FROM THERMUS AQUATICUS | ||||||
![]() | SIGNAL SEQUENCE RECOGNITION PROTEIN FFH | ||||||
![]() | SIGNAL RECOGNITION / FFH / SRP / GTPASE / SIGNAL RECOGNITION PARTICLE / GDP | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Freymann, D.M. / Stroud, R.M. / Walter, P. | ||||||
![]() | ![]() 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: ![]() Title: Crystal Structure of the Signal Sequence Binding Subunit of the Signal Recognition Particle Authors: Keenan, R.J. / Freymann, D.M. / Walter, P. / Stroud, R.M. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.2 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.6 KB | Display | ![]() |
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Full document | ![]() | 782.2 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ng1C ![]() 3ng1C ![]() 1ffhS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32199.199 Da / Num. of mol.: 1 / Fragment: NG GTPASE FRAGMENT / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-GDP / | ||
#3: Chemical | ChemComp-DIO / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.91 % | ||||||||||||||||||||
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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: ![]() |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 12, 1996 / Details: YALE MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→20 Å / Num. obs: 18481 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.02→2.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.284 / % possible all: 93 |
Reflection shell | *PLUS % possible obs: 92.8 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1FFH Resolution: 2.02→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 WAS APPLIED. THE DATA QUALITY AND COMPLETENESS BEYOND 2.3 A WERE AFFECTED BY A STRONG ICE RING. THE ELECTRON DENSITY MAPS WERE SOMEWHAT NOISIER THAN WOULD BE ...Details: A BULK SOLVENT CORRECTION WAS APPLIED. THE DATA QUALITY AND COMPLETENESS BEYOND 2.3 A WERE AFFECTED BY A STRONG ICE RING. THE ELECTRON DENSITY MAPS WERE SOMEWHAT NOISIER THAN WOULD BE EXPECTED FOR A STRUCTURE AT THIS RESOLUTION. SEVERAL MAIN CHAIN ATOMS OF THE FOLLOWING SURFACE EXPOSED STRETCHES ARE POORLY DEFINED IN THE ELECTRON DENSITY MAP: 1) PHE 2 - GLN 3, 2) GLY 18 - GLU 25, 3) GLN 63 - GLU 66, AND 4) ALA 251 - ARG 252. THEY ARE CHARACTERIZED BY HIGH TEMPERATURE FACTORS AND ARE PROBABLY MOBILE.
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Displacement parameters | Biso mean: 41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.02→2.08 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 16898 / Num. reflection Rfree: 1320 / Rfactor Rfree: 0.291 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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