+Open data
-Basic information
Entry | Database: PDB / ID: 2ot9 | ||||||
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Title | Crystal structure of YaeQ protein from Pseudomonas syringae | ||||||
Components | Hypothetical protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / YaeQ protein / Pseudomonas syringae / PSI-2 / Protein Structure Initiative / MCSG / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information Restriction endonuclease-like alpha-beta roll fold / Restriction endonuclease-like alpha-beta roll domain / YaeQ / YaeQ superfamily / YaeQ protein / YaeQ / Restriction endonuclease type II-like / Roll / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pseudomonas syringae pv. tomato (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å | ||||||
Authors | Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of YaeQ protein from Pseudomonas syringae Authors: Wu, R. / Clancy, S. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ot9.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ot9.ent.gz | 37.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ot9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ot9_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 2ot9_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 2ot9_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 2ot9_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ot/2ot9 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/2ot9 | 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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Unit cell |
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Details | This protein exists as a monomer |
-Components
#1: Protein | Mass: 20899.182 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: PSPTO_1487 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q886T9 |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-SRT / |
#4: 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: 2.32 Å3/Da / Density % sol: 46.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.5M K/Na Tartrate, 0.2M LiSO4, 10% PEG3350, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. all: 14451 / Num. obs: 14144 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 43.8 |
Reflection shell | Resolution: 1.97→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1421 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.97→48.22 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.254 / SU ML: 0.105 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.164 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.673 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→48.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 20.6218 Å / Origin y: 58.352 Å / Origin z: 7.5879 Å
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