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- PDB-3i7m: N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis. -
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Open data
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Basic information
Entry | Database: PDB / ID: 3i7m | ||||||
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Title | N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis. | ||||||
![]() | Xaa-Pro dipeptidase | ||||||
![]() | HYDROLASE / structural genomics / APC64794.2 / Xaa-Pro dipeptidase / Metallo peptidase / Creatinase/Prolidase N-terminal domain / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osipiuk, J. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: X-ray crystal structure of N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis. Authors: Osipiuk, J. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A.M. / 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 | ![]() | 43.7 KB | Display | ![]() |
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PDB format | ![]() | 33.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.7 KB | Display | ![]() |
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Full document | ![]() | 428.5 KB | Display | |
Data in XML | ![]() | 10.2 KB | Display | |
Data in CIF | ![]() | 14.6 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: 16122.450 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris buffer, 0.2 M ammonium sulfate, 25% PEG-3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 29, 2009 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→36.5 Å / Num. all: 22642 / Num. obs: 22642 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.561 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.46→1.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.05 / Num. unique all: 1115 / Χ2: 0.987 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 50.09 Å2 / Biso mean: 16.355 Å2 / Biso min: 5.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.46→36.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.456→1.494 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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