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Yorodumi- PDB-7epk: Crystal Structure of Signal Recognition Particle 54 kDa protein (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7epk | ||||||
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Title | Crystal Structure of Signal Recognition Particle 54 kDa protein (SRP54) from Aeropyrum pernix K1 in Complex with GDP | ||||||
Components | Signal recognition particle 54 kDa protein | ||||||
Keywords | HYDROLASE / SRP54-GDP complex / Aeropyrum pernix K1 / Crenarchaea | ||||||
Function / homology | Function and homology information signal recognition particle / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / GTPase activity / GTP binding Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Xie, Y. / Zhang, B. / Liu, J. | ||||||
Citation | Journal: To be published Title: Crystal Structure of Signal Recognition Particle 54 kDa protein (SRP54) from Aeropyrum pernix K1 in Complex with GDP Authors: Xie, Y. / Zhang, B. / Liu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7epk.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7epk.ent.gz | 73.7 KB | Display | PDB format |
PDBx/mmJSON format | 7epk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7epk_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7epk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7epk_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 7epk_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/7epk ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7epk | HTTPS FTP |
-Related structure data
Related structure data | 3kl4S 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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Unit cell |
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-Components
#1: Protein | Mass: 49196.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (archaea) Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1 Gene: srp54, APE_1735 / Plasmid: pET-11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9YB62 |
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#2: Chemical | ChemComp-GDP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 200 mM KH2PO4, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→41.28 Å / Num. obs: 15103 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rsym value: 0.049 / Net I/σ(I): 20.51 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.29 / Num. unique obs: 1400 / Rsym value: 0.303 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KL4 Resolution: 2.7→41.28 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.92 / SU B: 16.629 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.255 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 169.2 Å2 / Biso mean: 72.499 Å2 / Biso min: 29.12 Å2
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Refinement step | Cycle: final / Resolution: 2.7→41.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0
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