+Open data
-Basic information
Entry | Database: PDB / ID: 1qy9 | ||||||
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Title | Crystal structure of E. coli Se-MET protein YDDE | ||||||
Components | HYPOTHETICAL PROTEIN yddE | ||||||
Keywords | UNKNOWN FUNCTION / PUTATIVE PHENAZINE BIOSYNTHESIS PROTEIN / EPIMERASE / ANTIBIOTIC BIOSYNTHESIS PROTEIN / STRUCTURAL GENOMICS | ||||||
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 / SAD / Resolution: 2.05 Å | ||||||
Authors | Grassick, A. / Sulzenbacher, G. / Roig-Zamboni, V. / Campanacci, V. / Cambillau, C. / Bourne, Y. | ||||||
Citation | Journal: Proteins / Year: 2004 Title: Crystal structure of E. coli yddE protein reveals a striking homology with diaminopimelate epimerase Authors: Grassick, A. / Sulzenbacher, G. / Roig-Zamboni, V. / Campanacci, V. / Cambillau, C. / Bourne, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qy9.cif.gz | 242.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qy9.ent.gz | 203.7 KB | Display | PDB format |
PDBx/mmJSON format | 1qy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qy9_validation.pdf.gz | 465.9 KB | Display | wwPDB validaton report |
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Full document | 1qy9_full_validation.pdf.gz | 475.1 KB | Display | |
Data in XML | 1qy9_validation.xml.gz | 48.1 KB | Display | |
Data in CIF | 1qy9_validation.cif.gz | 69.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/1qy9 ftp://data.pdbj.org/pub/pdb/validation_reports/qy/1qy9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32639.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YDDE / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(DE3)pLysS / References: UniProt: P37757 #2: Chemical | #3: Chemical | ChemComp-OH / | #4: 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: 2.6 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 12% MPEG 5000, 0.2 M SODIUM ACETATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.954 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2002 |
Radiation | Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. obs: 80627 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.578 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.184 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.103 Å / Total num. of bins used: 20 /
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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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