[English] 日本語
Yorodumi- PDB-3i7m: N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis. -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i7m | ||||||
---|---|---|---|---|---|---|---|
Title | N-terminal domain of Xaa-Pro dipeptidase from Lactobacillus brevis. | ||||||
Components | Xaa-Pro dipeptidase | ||||||
Keywords | 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 | Function and homology information | ||||||
Biological species | Lactobacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.46 Å | ||||||
Authors | Osipiuk, J. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3i7m.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3i7m.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 3i7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/3i7m ftp://data.pdbj.org/pub/pdb/validation_reports/i7/3i7m | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16122.450 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis (bacteria) / Strain: ATCC 367 / Gene: LVIS_1204 / Plasmid: pET15b modified / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03R62 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.49 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.46→36.5 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 0.24 / SU B: 2.605 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→36.5 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.456→1.494 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|