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- PDB-2p0t: Structural Genomics, the crystal structure of a conserved putativ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2p0t | ||||||
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Title | Structural Genomics, the crystal structure of a conserved putative protein from Pseudomonas syringae pv. tomato str. DC3000 | ||||||
![]() | UPF0307 protein PSPTO_4464 | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC85033 / conserved putative protein / Pseudomonas syringae pv. tomato str. DC3000 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG | ||||||
Function / homology | ![]() PSPTO4464-like domains / Ribosome-associated, YjgA / PSPTO4464-like domain superfamily / Protein of unknown function (DUF615) / Diphtheria Toxin Repressor; domain 2 / Orthogonal Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tan, K. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of a conserved putative protein from Pseudomonas syringae pv. tomato str. DC3000 Authors: Tan, K. / Bigelow, L. / Clancy, S. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT IS EXPERIMENTALLY UNKNOWN. THE MONOMERIC ASSEMBLY OF THE BIOLOGICAL UNIT SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.8 KB | Display | ![]() |
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PDB format | ![]() | 31.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.2 KB | Display | ![]() |
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Full document | ![]() | 459.9 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | Experimentally unknown |
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Components
#1: Protein | Mass: 20540.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Pseudomonas syringae group genomosp. 3 / Strain: DC3000 / Gene: PSPTO_4464 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG1000, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2006 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→41.45 Å / Num. all: 9156 / Num. obs: 9156 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 44 |
Reflection shell | Resolution: 2.19→2.28 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2 / Num. unique all: 846 / % possible all: 94.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 61.163 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→41.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.25 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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