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Yorodumi- PDB-3i1e: Crystal Structure of the PDZ domain of the SdrC-like Protein (Lin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i1e | ||||||
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Title | Crystal Structure of the PDZ domain of the SdrC-like Protein (Lin2157) from Listeria innocua, Northeast Structural Genomics Consortium Target LkR136C | ||||||
Components | Lin2157 protein | ||||||
Keywords | structural genomics / unknown function / alpha-beta protein. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information endopeptidase La / ATP-dependent peptidase activity / protein catabolic process / serine-type endopeptidase activity / proteolysis / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Listeria innocua (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Nair, R. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target LkR136C Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Lee, D. / Everett, J.K. / Nair, R. / 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 | 3i1e.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i1e.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 3i1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/3i1e ftp://data.pdbj.org/pub/pdb/validation_reports/i1/3i1e | HTTPS FTP |
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-Related structure data
Related structure data | 3i18S S: Starting model for refinement |
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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: 9944.258 Da / Num. of mol.: 2 / Fragment: PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Gene: lin2157 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q929W6 #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: 2.11 Å3/Da / Density % sol: 41.64 % |
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Crystal grow | Temperature: 291 K / Method: microbatch, under oil / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 100mM MES (pH 6), 40% PEG 400, and 100mM MgSO4., Microbatch, under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97853 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. all: 7151 / Num. obs: 7080 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 65.3 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.124 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.6 / Num. unique all: 682 / Rsym value: 0.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3I18 Resolution: 2.91→18.94 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1063672.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.811 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.91→18.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
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