[English] 日本語
Yorodumi- PDB-2qmi: Structure of the octameric penicillin-binding protein homologue f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qmi | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi | ||||||
Components | Pbp related beta-lactamase | ||||||
Keywords | HYDROLASE / PAB87 / OCTAMER / LU-HPDO3A / PBP / ARCHAEA | ||||||
Function / homology | Function and homology information Pab87 octamerisation domain / Pab87 octamerisation domain / Pab87 octamerisation domain superfamily / Pab87 octamerisation domain / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Lipocalin / Beta-lactamase/transpeptidase-like ...Pab87 octamerisation domain / Pab87 octamerisation domain / Pab87 octamerisation domain superfamily / Pab87 octamerisation domain / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Lipocalin / Beta-lactamase/transpeptidase-like / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Delfosse, V. / Girard, E. / Moulinier, L. / Schultz, P. / Mayer, C. | ||||||
Citation | Journal: Plos One / Year: 2009 Title: Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family Authors: Delfosse, V. / Girard, E. / Birck, C. / Delmarcelle, M. / Delarue, M. / Poch, O. / Schultz, P. / Mayer, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qmi.cif.gz | 735.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qmi.ent.gz | 606.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qmi_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2qmi_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 2qmi_validation.xml.gz | 154.6 KB | Display | |
Data in CIF | 2qmi_validation.cif.gz | 219.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/2qmi ftp://data.pdbj.org/pub/pdb/validation_reports/qm/2qmi | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 50503.371 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Strain: GE5 / Gene: pbp / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9V2D6, beta-lactamase #2: Chemical | ChemComp-LU / #3: Chemical | ChemComp-DO3 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.02M calcium chloride dihydrate, 0.1M sodium acetate trihydrate, 30% MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.34029 Å | ||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2007 | ||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.34029 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||
Reflection | Av σ(I) over netI: 17.36 / Number: 1542549 / Rmerge(I) obs: 0.081 / D res high: 2.2 Å / Num. obs: 198621 / % possible obs: 95.9 | ||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| ||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→30 Å / Num. all: 198053 / Num. obs: 198053 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.08 / Net I/σ(I): 17.4 | ||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 7.2 / Num. unique all: 28540 / Rsym value: 0.289 / % possible all: 93.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.2→30 Å / Isotropic thermal model: Restrained / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 37.475 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.451 Å2
| ||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.28 Å
| ||||||||||||||||||||||||||||
Xplor file |
|