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- PDB-4jx2: Crystal structure of a putative secreted protein (lpg1979) from L... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4jx2 | ||||||
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Title | Crystal structure of a putative secreted protein (lpg1979) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.65 A resolution | ||||||
![]() | hypothetical protein![]() | ||||||
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Function / homology | Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2710 / Domain of unknown function DUF5624 / Domain of unknown function (DUF5624) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / DI(HYDROXYETHYL)ETHER / ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of a hypothetical protein (lpg1979) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.65 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333.9 KB | Display | ![]() |
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PDB format | ![]() | 277.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 48992.895 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Philadelphia 1 / Gene: lpg1979, YP_095995.1 / Plasmid: SpeedET / Production host: ![]() ![]() ![]() |
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-Non-polymers , 6 types, 282 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ChemComp-PGE / ![]() #5: Chemical | ![]() #6: Chemical | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | THE CONSTRUCT (22-375) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (22-375) WAS EXPRESSED WITH A PURIFICATI |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.39 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M lithium sulfate, 40.0% polyethylene glycol 400, 0.2M lithium sulfate, 40.0% polyethylene glycol 400, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2013 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.65→47.97 Å / Num. obs: 33147 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 56.91 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.63 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PEG FRAGMENTS, CL AND SO4 MODELED ARE PRESENT IN CRYSTALLIZATION CONDITION. 5.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS).
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Displacement parameters | Biso max: 157.17 Å2 / Biso mean: 49.4094 Å2 / Biso min: 19.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.285 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→47.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.73 Å / Total num. of bins used: 17
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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