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Yorodumi- PDB-1sdj: X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sdj | |||||||||
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Title | X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25. | |||||||||
Components | Hypothetical protein yddE | |||||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | |||||||||
Function / homology | Function and homology information Isomerases; Racemases and epimerases / biosynthetic process / isomerase activity / protein homodimerization activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | |||||||||
Authors | Kuzin, A.P. / Edstrom, W. / Skarina, T. / Korniyenko, Y. / Savchenko, A. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sdj.cif.gz | 76.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sdj.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 1sdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sdj_validation.pdf.gz | 441.7 KB | Display | wwPDB validaton report |
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Full document | 1sdj_full_validation.pdf.gz | 448.3 KB | Display | |
Data in XML | 1sdj_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 1sdj_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/1sdj ftp://data.pdbj.org/pub/pdb/validation_reports/sd/1sdj | HTTPS FTP |
-Related structure data
Related structure data | 1u1vC 1u1wC 1u1xC 1xuaC 1xubC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Escherichia coli (E. coli) / Gene: YDDE, B1464 / Plasmid: PET15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P37757 | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97929, 0.97970, 0.97702 | ||||||||||||
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 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→19.87 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 591533.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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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: 0.26 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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