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- PDB-3ge2: Crystal structure of putative lipoprotein SP_0198 from Streptococ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ge2 | ||||||
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Title | Crystal structure of putative lipoprotein SP_0198 from Streptococcus pneumoniae | ||||||
![]() | Lipoprotein, putative | ||||||
![]() | LIPOPROTEIN / beta-barrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() Domain of unknown function DUF3642, lipoprotein / Bacterial lipoprotein / Lipocalin - #50 / D-aminopeptidase/lipoprotein domain superfamily / Lipocalin / Beta Barrel / Mainly Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Zhang, R. / Joachimiak, G. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal Structure of Putative Lipoprotein SP_0198 from Streptococcus pneumoniae Authors: Kim, Y. / Zhang, R. / Joachimiak, G. / Gornicki, P. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.7 KB | Display | ![]() |
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PDB format | ![]() | 37.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.2 KB | Display | ![]() |
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Full document | ![]() | 447.2 KB | Display | |
Data in XML | ![]() | 7.6 KB | Display | |
Data in CIF | ![]() | 9.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14113.791 Da / Num. of mol.: 1 / Fragment: UNP residues 26-152 Source method: isolated from a genetically manipulated source Details: N-terminal MBP-fusion with TVMV protease cut-site which is cleaved in vivo and a 6-His tag with TEV protease cut site Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-K / | ||||
#3: Chemical | ChemComp-CL / | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | THE PROTEIN SEQUENCE PROVIDED BY AUTHORS IS THE SEQUENCE OF THE PROTEIN USED FOR CRYSTALLIZATION. ...THE PROTEIN SEQUENCE PROVIDED BY AUTHORS IS THE SEQUENCE OF THE PROTEIN USED FOR CRYSTALLIZ | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.71 Å3/Da / Density % sol: 66.87 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M Sodium acetate trihydrate pH 4.5, 2.0 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40.9 Å / Num. all: 11211 / Num. obs: 11211 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 43.59 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 3 / Num. unique all: 537 / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.727 Å2 / ksol: 0.399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.203→37.421 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Origin x: 25.2015 Å / Origin y: 31.4046 Å / Origin z: 32.0837 Å
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Refinement TLS group | Selection details: chain A |