[English] 日本語
Yorodumi- PDB-5hif: Crystal structure of a reconstructed lactonase ancestor, Anc1-MPH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hif | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a reconstructed lactonase ancestor, Anc1-MPH, of the bacterial methyl parathion hydrolase, MPH. | ||||||
Components | reconstructed lactonase ancestor, Anc1-MPH | ||||||
Keywords | HYDROLASE / ancestral reconstruction / lactonase / methyl parathion hydrolase | ||||||
Function / homology | Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 4-Layer Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Baier, F. / Carr, P.D. / Jackson, C.J. | ||||||
Citation | Journal: To Be Published Title: to be published Authors: Baier, F. / Carr, P.D. / Jackson, C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5hif.cif.gz | 138.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5hif.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 5hif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/5hif ftp://data.pdbj.org/pub/pdb/validation_reports/hi/5hif | HTTPS FTP |
---|
-Related structure data
Related structure data | 1p9eS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: -4 - 294 / Label seq-ID: 1 - 299
|
-Components
#1: Protein | Mass: 31517.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b Details (production host): N-terminal MBP-tag with TEV cleavage site Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (D3) / References: EC: 3.1.1.35 #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.92 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Magnesium acetate terahydrate 20% PEG 3350 10mM Tris/HCl 50mM NaCl 0.1mM ZnCl2 PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: oxford cryostream |
---|---|
Diffraction source | Source: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2015 / Details: MARMUX |
Radiation | Monochromator: micro source / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→33.6 Å / Num. obs: 78672 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 11.078 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 4.9 / % possible all: 90.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1p9e.ent Resolution: 1.6→33.6 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.544 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 18.322 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→33.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|