[English] 日本語
Yorodumi- PDB-6vim: P. putida mandelate racemase co-crystallized with phenylboronic acid -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vim | ||||||
---|---|---|---|---|---|---|---|
Title | P. putida mandelate racemase co-crystallized with phenylboronic acid | ||||||
Components | Mandelate racemase | ||||||
Keywords | ISOMERASE/INHIBITOR / Inhibitor / Boronate / ISOMERASE / ISOMERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information mandelate racemase / mandelate racemase activity / mandelate catabolic process / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Grandinetti, L. / Sharma, A.N. / Bearne, S.L. / St Maurice, M. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2020 Title: Potent Inhibition of Mandelate Racemase by Boronic Acids: Boron as a Mimic of a Carbon Acid Center. Authors: Sharma, A.N. / Grandinetti, L. / Johnson, E.R. / St Maurice, M. / Bearne, S.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6vim.cif.gz | 765.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6vim.ent.gz | 501.5 KB | Display | PDB format |
PDBx/mmJSON format | 6vim.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/6vim ftp://data.pdbj.org/pub/pdb/validation_reports/vi/6vim | HTTPS FTP |
---|
-Related structure data
Related structure data | 3uxkS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 41304.621 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlA / Production host: Escherichia coli (E. coli) / References: UniProt: P11444, mandelate racemase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-PBC / #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.42 % / Description: cube-like crystals (~50 um x 40 um x 40 um) |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: The reservoir solution consisted of PEG 4000 (10% w/v) and Bis-Tris Propane (BTP; 50 mM, pH 7.0). The protein solution consisted of 6 mg/mL P. putida MR, 1.0 mM phenylboronic acid, 3.3 mM ...Details: The reservoir solution consisted of PEG 4000 (10% w/v) and Bis-Tris Propane (BTP; 50 mM, pH 7.0). The protein solution consisted of 6 mg/mL P. putida MR, 1.0 mM phenylboronic acid, 3.3 mM MgCl2, and 50 mM HEPES buffer (pH 7.5). The protein solution and reservoir solution were mixed in a 1:1 ratio to a final volume of 10 uL PH range: 7.0 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2→116.57 Å / Num. obs: 262707 / % possible obs: 99.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 19.69 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 26100 / CC1/2: 0.782 / % possible all: 99.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UXK Resolution: 2→116.37 Å / SU ML: 0.204 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6143 / Stereochemistry target values: GeoStd + Monomer Library
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→116.37 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|