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Yorodumi- PDB-4xco: Signal-sequence induced conformational changes in the signal reco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xco | ||||||
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Title | Signal-sequence induced conformational changes in the signal recognition particle | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / SIGNAL RECOGNITION PARTICLE / SIGNAL SEQUENCE / RECOMBINANT FUSION PROTEIN / RNA STRUCTURE | ||||||
Function / homology | Function and homology information signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / molecular adaptor activity / GTPase activity / GTP binding / ATP hydrolysis activity Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Hainzl, T. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat Commun / Year: 2015 Title: Signal-sequence induced conformational changes in the signal recognition particle. Authors: Hainzl, T. / Sauer-Eriksson, A.E. #1: Journal: Nat. Struct. Mol. Biol. / Year: 2011 Title: Structural basis of signal-sequence recognition by the signal recognition particle. Authors: Hainzl, T. / Huang, S. / Merilainen, G. / Brannstrom, K. / Sauer-Eriksson, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xco.cif.gz | 334.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xco.ent.gz | 265.1 KB | Display | PDB format |
PDBx/mmJSON format | 4xco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/4xco ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xco | HTTPS FTP |
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-Related structure data
Related structure data | 3ndbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-RNA chain , 1 types, 2 molecules ME
#1: RNA chain | Mass: 31162.604 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Production host: synthetic construct (others) / References: GenBank: 6626255 |
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-Signal recognition particle ... , 2 types, 4 molecules ABCD
#2: Protein | Mass: 10376.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: srp19, MJ1034 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C41 / References: UniProt: Q58440 #3: Protein | Mass: 19206.736 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: srp54, MJ0101, mj0101, srp54 / Plasmid: pNZ8048 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q57565 |
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-Non-polymers , 3 types, 85 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: The complex (3mg/ml) was mixed 1:1 with 35% 2-Methyl-2,4-pentanediol (MPD), 200 mM NaCl, 80 mM MgCl2, 100 mM sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→48.025 Å / Num. obs: 28330 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.9→3.08 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 1.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ndb Resolution: 2.9→48.025 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→48.025 Å
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Refine LS restraints |
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LS refinement shell |
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