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Yorodumi- PDB-3pes: Crystal structure of uncharacterized protein from Pseudomonas pha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pes | ||||||
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Title | Crystal structure of uncharacterized protein from Pseudomonas phage YuA | ||||||
Components | Uncharacterized protein gp49 | ||||||
Keywords | Structural genomics / Unknown function / PSI2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | GMP Synthetase; Chain A, domain 3 - #260 / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein gp49 Function and homology information | ||||||
Biological species | Pseudomonas phage YuA (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å | ||||||
Authors | Nocek, B. / Stein, A. / Evdokimove, A. / Egorova, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of uncharacterized protein from Pseudomonas phage YuA Authors: Nocek, B. / Stein, A. / Evdokimove, A. / Egorova, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pes.cif.gz | 86.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pes.ent.gz | 70.9 KB | Display | PDB format |
PDBx/mmJSON format | 3pes.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pes_validation.pdf.gz | 424.1 KB | Display | wwPDB validaton report |
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Full document | 3pes_full_validation.pdf.gz | 425.1 KB | Display | |
Data in XML | 3pes_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 3pes_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pe/3pes ftp://data.pdbj.org/pub/pdb/validation_reports/pe/3pes | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. |
-Components
#1: Protein | Mass: 9878.829 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas phage YuA (virus) / Gene: gp49 / Plasmid: pet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: A9J573 #2: 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: 2.13 Å3/Da / Density % sol: 42.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M SPG, 25 % Peg3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010 / Details: mirrors |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→40 Å / Num. all: 40040 / Num. obs: 39941 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3893 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.3→23.23 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.864 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.063 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.953 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→23.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.297→1.331 Å / Total num. of bins used: 20
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