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Yorodumi- PDB-3owq: X-Ray Structure of Lin1025 protein from Listeria innocua, Northea... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3owq | ||||||
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Title | X-Ray Structure of Lin1025 protein from Listeria innocua, Northeast Structural Genomics Consortium Target LkR164 | ||||||
Components | Lin1025 protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | LCP protein / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / membrane => GO:0016020 / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Lin1025 protein Function and homology information | ||||||
Biological species | Listeria innocua (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.606 Å | ||||||
Authors | Kuzin, A. / Su, M. / Lew, S. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. ...Kuzin, A. / Su, M. / Lew, S. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / 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 LkR164 Authors: Kuzin, A. / Su, M. / Lew, S. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / 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 | 3owq.cif.gz | 366.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3owq.ent.gz | 312.6 KB | Display | PDB format |
PDBx/mmJSON format | 3owq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3owq_validation.pdf.gz | 472.8 KB | Display | wwPDB validaton report |
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Full document | 3owq_full_validation.pdf.gz | 516.7 KB | Display | |
Data in XML | 3owq_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 3owq_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/3owq ftp://data.pdbj.org/pub/pdb/validation_reports/ow/3owq | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35885.699 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin1025 / References: UniProt: Q92CZ6 #2: Chemical | #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 grow | Method: vapor diffusion, hanging drop / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: LiCl 0.1M, PEG1K 22%, MES 0.1M, VAPOR DIFFUSION, HANGING DROP |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9789 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2010 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 58846 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 46.72 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.606→28.332 Å / SU ML: 0.33 / σ(F): 1.36 / Phase error: 30.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.613 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.606→28.332 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.3844 Å / Origin y: -0.0362 Å / Origin z: 26.5264 Å
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Refinement TLS group | Selection details: all |