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- PDB-1sdj: X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1sdj | |||||||||
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Title | X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25. | |||||||||
![]() | Hypothetical protein yddE![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kuzin, A.P. / Edstrom, W. / Skarina, T. / Korniyenko, Y. / Savchenko, A. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | |||||||||
![]() | ![]() Title: Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens. Authors: Blankenfeldt, W. / Kuzin, A.P. / Skarina, T. / Korniyenko, Y. / Tong, L. / Bayer, P. / Janning, P. / Thomashow, L.S. / Mavrodi, D.V. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.1 KB | Display | ![]() |
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PDB format | ![]() | 56.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1u1vC ![]() 1u1wC ![]() 1u1xC ![]() 1xuaC ![]() 1xubC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 34074.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SO4 / ![]() #3: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.73 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | *PLUS Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4.4 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→20 Å / Num. all: 140762 / Num. obs: 32871 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.247 / Num. unique all: 2943 / Rsym value: 0.247 / % possible all: 85.6 | ||||||||||||
Reflection | *PLUS % possible obs: 89.5 % | ||||||||||||
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 85.6 % / Redundancy: 27 % / Mean I/σ(I) obs: 3 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 38.7607 Å2 / ksol: 0.333235 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree![]() | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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