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Yorodumi- PDB-3ka5: Crystal structure of Ribosome-associated protein Y (PSrp-1) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ka5 | ||||||
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Title | Crystal structure of Ribosome-associated protein Y (PSrp-1) from Clostridium acetobutylicum. Northeast Structural Genomics Consortium target id CaR123A | ||||||
Components | Ribosome-associated protein Y (PSrp-1) | ||||||
Keywords | CHAPERONE / Ribosome-associated protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium acetobutylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Seetharaman, J. / Neely, H. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Neely, H. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Ribosome-associated protein Y (PSrp-1) from Clostridium acetobutylicum Authors: Seetharaman, J. / Neely, H. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ka5.cif.gz | 33.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ka5.ent.gz | 25.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ka5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ka5_validation.pdf.gz | 430.4 KB | Display | wwPDB validaton report |
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Full document | 3ka5_full_validation.pdf.gz | 432.6 KB | Display | |
Data in XML | 3ka5_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 3ka5_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/3ka5 ftp://data.pdbj.org/pub/pdb/validation_reports/ka/3ka5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 7776.408 Da / Num. of mol.: 2 / Fragment: sequence database residues 117-173 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_C2847, Ordered Locus Names: CA_C2847 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97F93 #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: 2.25 Å3/Da / Density % sol: 45.45 % |
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Crystal grow | Temperature: 277 K / pH: 4.2 Details: 0.1M KSCN, 0.1M Na3Citrate pH 4.2, 20% PEG 4K, microbatch under oil method, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 24939 / Num. obs: 24939 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.395 / Num. unique all: 1154 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→32.39 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 151523.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.309 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→32.39 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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