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- PDB-3cp3: Crystal structure of conserved protein of unknown function DIP187... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3cp3 | ||||||
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Title | Crystal structure of conserved protein of unknown function DIP1874 from Corynebacterium diphtheriae | ||||||
![]() | Uncharacterized protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta fold / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Pyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / ACETIC ACID / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal structure of the conserved protein of unknown function DIP1874 from Corynebacterium diphtheriae. Authors: Kim, Y. / Wu, R. / Clancy, S. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.5 KB | Display | ![]() |
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PDB format | ![]() | 29.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.7 KB | Display | ![]() |
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Full document | ![]() | 448.3 KB | Display | |
Data in XML | ![]() | 8.5 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 | AUTHORS STATE THAT THE BIOLOGICAL UNIT COULD BE EITHER DIMER OR TETRAMER |
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Components
#1: Protein | Mass: 16845.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Corynebacterium diphtheriae / Strain: NCTC 13129 / Biotype gravis / Gene: DIP1874 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ACY / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: 30% PEG 8000, 0.1 M Acetate pH 4.5, 0.2 M Lithium sulfate, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-3 / Detector: CCD / Date: Jun 4, 2007 / 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: 1.98→50.9 Å / Num. all: 11597 / Num. obs: 11597 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 5.77 / Num. unique all: 905 / % possible all: 76.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SAD phased model of the L37M mutant of the same protein, P1 space group Resolution: 2→29.68 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.228 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 38.883 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 55.009 Å / Origin y: -10.1855 Å / Origin z: 24.0175 Å
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