[English] 日本語
Yorodumi- PDB-2zvd: Crystal structure of Pseudomonas sp. MIS38 lipase in an open conf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zvd | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Pseudomonas sp. MIS38 lipase in an open conformation | ||||||
Components | Lipase | ||||||
Keywords | HYDROLASE / Family I.3 lipase / Beta roll / Calcium binding protein / RTX protein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas (RNA similarity group I) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Angkawidjaja, C. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: X-ray Crystallographic and MD Simulation Studies on the Mechanism of Interfacial Activation of a Family I.3 Lipase with Two Lids Authors: Angkawidjaja, C. / Matsumura, H. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2zvd.cif.gz | 269.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2zvd.ent.gz | 212.1 KB | Display | PDB format |
PDBx/mmJSON format | 2zvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/2zvd ftp://data.pdbj.org/pub/pdb/validation_reports/zv/2zvd | HTTPS FTP |
---|
-Related structure data
Related structure data | 3a6zC 3a70C 2z8xS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 64563.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Strain: MIS38 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: Q9RBY1, triacylglycerol lipase #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.06 Å3/Da / Density % sol: 59.74 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2M ammonium acetate, 0.1M Tris-HCl, pH8.5, 30% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Oct 22, 2008 / Details: mirrors |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 171224 / Num. obs: 95813 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.103 / Rsym value: 0.077 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 11 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 6.3 / Num. unique all: 9353 / Rsym value: 0.401 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Z8X Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.803 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.161 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 22.724 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→40 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.151→2.207 Å / Total num. of bins used: 20
|