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Yorodumi- PDB-3lyv: Crystal structure of a domain of ribosome-associated factor Y fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3lyv | ||||||
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Title | Crystal structure of a domain of ribosome-associated factor Y from streptococcus pyogenes serotype M6. Northeast Structural Genomics Consortium target id DR64A | ||||||
Components | Ribosome-associated factor Y | ||||||
Keywords | CHAPERONE / ribosomal protein S30Ae family / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å | ||||||
Authors | Seetharaman, J. / Neely, H. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Seetharaman, J. / Neely, H. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a domain of ribosome-associated factor Y from streptococcus pyogenes serotype M6. Northeast Structural Genomics Consortium target id DR64A Authors: Seetharaman, J. / Neely, H. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.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 | 3lyv.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lyv.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 3lyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3lyv_validation.pdf.gz | 470.3 KB | Display | wwPDB validaton report |
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Full document | 3lyv_full_validation.pdf.gz | 484.7 KB | Display | |
Data in XML | 3lyv_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 3lyv_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/3lyv ftp://data.pdbj.org/pub/pdb/validation_reports/ly/3lyv | 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 7905.432 Da / Num. of mol.: 6 / Fragment: sequence database residues 126-182 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: serotype M6 / Gene: M6_Spy1371 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5XAQ7 |
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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: 2.43 Å3/Da / Density % sol: 49.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.14M (NH4)2SO4, 0.1M MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 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: 2.7→50 Å / Num. all: 27508 / Num. obs: 27508 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.059 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.7→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 24 / Num. unique all: 1387 / Rsym value: 0.322 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.7→47.22 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 156003.95 / 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: 56.2825 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 59.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→47.22 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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