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Open data
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Basic information
Entry | Database: PDB / ID: 6dlx | ||||||
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Title | FtsY-NG domain bound to fragment 3. | ||||||
![]() | Signal recognition particle receptor FtsY | ||||||
![]() | SIGNALING PROTEIN / SRP / SR receptor / FtsY / FBDD | ||||||
Function / homology | ![]() signal recognition particle binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / GTPase activity / GTP binding / protein homodimerization activity / ATP hydrolysis activity ...signal recognition particle binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / GTPase activity / GTP binding / protein homodimerization activity / ATP hydrolysis activity / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ataide, F.S. / Faoro, C. | ||||||
![]() | ![]() Title: Discovery of fragments that target key interactions in the signal recognition particle (SRP) as potential leads for a new class of antibiotics. Authors: Faoro, C. / Wilkinson-White, L. / Kwan, A.H. / Ataide, S.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 348.7 KB | Display | ![]() |
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PDB format | ![]() | 292.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 462.2 KB | Display | ![]() |
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Full document | ![]() | 467 KB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 35.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6cqpSC ![]() 6cs8C ![]() 6cvdC 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: 33101.043 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: A0A1M2TDP9, UniProt: P10121*PLUS #2: Chemical | ChemComp-GXY / #3: Chemical | ChemComp-NH4 / #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 297.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris pH 5.8, 25% PEG 3350, 165 mM ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.848→43.991 Å / Num. obs: 47444 / % possible obs: 99.36 % / Redundancy: 2 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.02828 / Rrim(I) all: 0.04 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.848→1.914 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6CQP Resolution: 1.848→43.991 Å / Cross valid method: FREE R-VALUE / σ(F): 7.52 / Phase error: 36.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.848→43.991 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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