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Open data
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Basic information
Entry | Database: PDB / ID: 2ffh | ||||||
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Title | THE SIGNAL SEQUENCE BINDING PROTEIN FFH FROM THERMUS AQUATICUS | ||||||
![]() | PROTEIN (FFH) | ||||||
![]() | PROTEIN TRANSPORT / FFH / SRP54 / SIGNAL RECOGNITION PARTICLE / GTPASE / M DOMAIN / RNA-BINDING / SIGNAL SEQUENCE-BINDING / HELIX-TURN-HELIX / PROTEIN TARGETING | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Keenan, R.J. / Freymann, D.M. / Walter, P. / Stroud, R.M. | ||||||
![]() | ![]() 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. #1: ![]() 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 | ![]() | 241.1 KB | Display | ![]() |
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PDB format | ![]() | 196.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399.8 KB | Display | ![]() |
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Full document | ![]() | 428.9 KB | Display | |
Data in XML | ![]() | 27.3 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ffhS S: Starting model for refinement |
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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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Details | The bacterial SRP contains one molecule of Ffh bound to one molecule of SRP RNA. |
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Components
#1: Protein | Mass: 46811.449 Da / Num. of mol.: 3 / Fragment: RESIDUES 1-425 / Mutation: A48T Source method: isolated from a genetically manipulated source Details: THE EXPRESSION INSERT WAS GENERATED BY PCR / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CD / #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PROTEIN AT 20 MG/ML IN 5 MM HEPES, PH 7.5. CRYSTALLIZED AT RT BY HANGING DROP VAPOR DIFFUSION USING 1.2 M SODIUM ACETATE, 0.12 M CADMIUM SULFATE, 0.1 M TRIS PH 8.5, 20 MM LITHIUM DODECYL ...Details: PROTEIN AT 20 MG/ML IN 5 MM HEPES, PH 7.5. CRYSTALLIZED AT RT BY HANGING DROP VAPOR DIFFUSION USING 1.2 M SODIUM ACETATE, 0.12 M CADMIUM SULFATE, 0.1 M TRIS PH 8.5, 20 MM LITHIUM DODECYL SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
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: PRINCETON 2K / Detector: CCD / Date: Jul 4, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 40702 / Num. obs: 36791 / % possible obs: 90.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.2→3.36 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3914 / % possible all: 79.6 |
Reflection shell | *PLUS % possible obs: 79.6 % |
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Processing
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Refinement | Method to determine structure: ![]() ![]() Starting model: PDB ENTRY 1FFH Resolution: 3.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The structure was refined using the maximum likelihood target with individual b-factor refinement and bulk solvent correction.
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Displacement parameters | Biso mean: 72.9 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→30 Å
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Refine LS restraints NCS | NCS model details: THROUGHOUT REFINEMENT TIGHT NCS RESTRAINTS WERE APPLIED SEPARATELY TO EACH OF THE THREE DOMAINS OF FFH -- N (RESIDUES 1-86), G (RESIDUES 87-307) AND M (RESIDUES 319-418). DURING ...NCS model details: THROUGHOUT REFINEMENT TIGHT NCS RESTRAINTS WERE APPLIED SEPARATELY TO EACH OF THE THREE DOMAINS OF FFH -- N (RESIDUES 1-86), G (RESIDUES 87-307) AND M (RESIDUES 319-418). DURING THE FINAL STAGES OF REBUILDING AND REFINEMENT, NCS RESTRAINTS WERE RELAXED FOR RESIDUES 271-279 (THE CLOSING LOOP), 295-307 (HINGE) AND 345-356 (C-TERMINAL HALF OF THE FINGER LOOP), WHICH ARE INVOLVED IN EITHER CRYSTALLOGRAPHIC OR NON- CRYSTALLOGRAPHIC PACKING CONTACTS. | |||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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