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- PDB-2r9i: Crystal structure of putative phage capsid protein domain from Co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2r9i | ||||||
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Title | Crystal structure of putative phage capsid protein domain from Corynebacterium diphtheriae | ||||||
![]() | Putative phage capsid protein | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Putative phage capsid domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Phage capsid / Phage capsid family / ATP synthase, gamma subunit, helix hairpin domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Putative phage capsid protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: The crystal structure of putative phage capsid protein domain from Corynebacterium diphtheriae. Authors: Wu, R. / Abdullah, J. / 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 | ![]() | 23 KB | Display | ![]() |
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PDB format | ![]() | 17.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 403.8 KB | Display | ![]() |
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Full document | ![]() | 406.5 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 4.4 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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Unit cell |
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Components
#1: Protein | Mass: 15520.618 Da / Num. of mol.: 1 / Fragment: N-terminal domain: Residues 1-138 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Species: Corynebacterium diphtheriae / Strain: NCTC 13129 / Biotype gravis / Gene: DIP0205 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Bis-tris propane pH 7.0, 3.5M Sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SBC-2 / Detector: CCD / Date: Aug 19, 2007 / 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: 2.6→50 Å / Num. all: 5692 / Num. obs: 5692 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Biso Wilson estimate: 80.16 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 46.2 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 21.1 % / Rmerge(I) obs: 0.798 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Residues 73-138 are missing in coordinates due to lack of electron density
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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: 74.252 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→32.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.9599 Å / Origin y: 48.9035 Å / Origin z: 6.9054 Å
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