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Yorodumi- PDB-2inw: Crystal structure of Q83JN9 from Shigella flexneri at high resolu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2inw | ||||||
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Title | Crystal structure of Q83JN9 from Shigella flexneri at high resolution. Northeast Structural Genomics Consortium target SfR137. | ||||||
Components | Putative structural protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q83JN9 X-Ray NESG SfR137 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shigella flexneri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Kuzin, A.P. / Su, M. / Jayaraman, S. / Vorobiev, S.M. / Wang, D. / Jiang, M. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Su, M. / Jayaraman, S. / Vorobiev, S.M. / Wang, D. / Jiang, M. / Cunningham, K. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Structure / Year: 2010 Title: Crystal Structures of Phd-Doc, HigA, and YeeU Establish Multiple Evolutionary Links between Microbial Growth-Regulating Toxin-Antitoxin Systems. Authors: Arbing, M.A. / Handelman, S.K. / Kuzin, A.P. / Verdon, G. / Wang, C. / Su, M. / Rothenbacher, F.P. / Abashidze, M. / Liu, M. / Hurley, J.M. / Xiao, R. / Acton, T. / Inouye, M. / Montelione, ...Authors: Arbing, M.A. / Handelman, S.K. / Kuzin, A.P. / Verdon, G. / Wang, C. / Su, M. / Rothenbacher, F.P. / Abashidze, M. / Liu, M. / Hurley, J.M. / Xiao, R. / Acton, T. / Inouye, M. / Montelione, G.T. / Woychik, N.A. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2inw.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2inw.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 2inw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2inw_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 2inw_full_validation.pdf.gz | 440.9 KB | Display | |
Data in XML | 2inw_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 2inw_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/2inw ftp://data.pdbj.org/pub/pdb/validation_reports/in/2inw | HTTPS FTP |
-Related structure data
Related structure data | 2h28C 2ictC 3kh2C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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: 14956.386 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: yeeU, SF2998, S_3203 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21) + Magic / References: UniProt: Q83JN9, UniProt: A0A0H2VX33*PLUS #2: Chemical | ChemComp-PO4 / | #3: 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: 2.15 Å3/Da / Density % sol: 42.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1M Kh2PO4, 0.1M MES, 20% PEG20K, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
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Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 26, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 77681 / Num. obs: 41154 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→19.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 144000.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.2607 Å2 / ksol: 0.325375 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→19.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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