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Yorodumi- PDB-6fpr: Co-translational folding intermediate dictates membrane targeting... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fpr | ||||||
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Title | Co-translational folding intermediate dictates membrane targeting of the signal recognition particle (SRP)- receptor | ||||||
Components | Signal recognition particle receptor FtsY | ||||||
Keywords | Membrane binding protein | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Karniel, A. / Mrusek, D. / Steinchen, W. / Dym, O. / Bange, G. / Bibi, E. | ||||||
Funding support | Israel, 1items
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Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Co-translational Folding Intermediate Dictates Membrane Targeting of the Signal Recognition Particle Receptor. Authors: Karniel, A. / Mrusek, D. / Steinchen, W. / Dym, O. / Bange, G. / Bibi, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fpr.cif.gz | 33.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fpr.ent.gz | 22.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fpr_validation.pdf.gz | 432.3 KB | Display | wwPDB validaton report |
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Full document | 6fpr_full_validation.pdf.gz | 432.4 KB | Display | |
Data in XML | 6fpr_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 6fpr_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/6fpr ftp://data.pdbj.org/pub/pdb/validation_reports/fp/6fpr | HTTPS FTP |
-Related structure data
Related structure data | 6fpkC 6fqdC 2qy9S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6928.821 Da / Num. of mol.: 2 / Fragment: N Terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: ftsY, b3464, JW3429 / Production host: Escherichia coli (E. coli) / References: UniProt: P10121 #2: 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: 3.32 Å3/Da / Density % sol: 62.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22% MPD NaCacodylate pH=6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953723 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953723 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→40.88 Å / Num. obs: 5435 / % possible obs: 99.65 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.099 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 781 / Rrim(I) all: 0.586 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QY9 Resolution: 2.65→19.93 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.939 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.303 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.734 Å2
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Refinement step | Cycle: 1 / Resolution: 2.65→19.93 Å
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Refine LS restraints |
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