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Yorodumi- PDB-3kav: Crystal Structure of THE MUTANT (L80M) PA2107 PROTEIN from Pseudo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kav | ||||||
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Title | Crystal Structure of THE MUTANT (L80M) PA2107 PROTEIN from Pseudomonas aeruginosa, Northeast Structural Genomics Consortium Target PaR198 | ||||||
Components | uncharacterized protein PA2107 | ||||||
Keywords | structural genomics / unknown function / all alpha-helical protein. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #360 / Protein of unknown function DUF326 / Domain of Unknown Function (DUF326) / Uncharacterized cysteine-rich protein YhjQ-like / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha / Four-helix bundle copper-binding protein Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target PaR198 Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / 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 | 3kav.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kav.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/3kav ftp://data.pdbj.org/pub/pdb/validation_reports/ka/3kav | HTTPS FTP |
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-Related structure data
-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: 15419.110 Da / Num. of mol.: 4 / Mutation: L80M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2107 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q9I208 #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: 2.07 Å3/Da / Density % sol: 40.59 % |
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Crystal grow | Temperature: 291 K / pH: 4.4 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 50 mM Na3Citrate (pH 4.4), 8% PEG4K, and 50 mM MgSO4. microbatch under oil , temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9787 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 2, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 33782 / Num. obs: 33749 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.062 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.311 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→19.97 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 258107.04 / 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: 67.2657 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.59 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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Xplor file |
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