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- PDB-4fp1: P. putida mandelate racemase co-crystallized with 3,3,3-trifluoro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fp1 | ||||||
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Title | P. putida mandelate racemase co-crystallized with 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl) propionic acid | ||||||
![]() | Mandelate racemase | ||||||
![]() | ISOMERASE/ISOMERASE INHIBITOR / Enolase superfamily enzyme / ISOMERASE-ISOMERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lietzan, A.D. / St.Maurice, M. | ||||||
![]() | ![]() Title: Potent inhibition of mandelate racemase by a fluorinated substrate-product analogue with a novel binding mode. Authors: Nagar, M. / Lietzan, A.D. / St Maurice, M. / Bearne, S.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159.7 KB | Display | ![]() |
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PDB format | ![]() | 124 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.3 KB | Display | ![]() |
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Full document | ![]() | 467.5 KB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 46.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4hncC ![]() 4m6uC ![]() 2mnrS ![]() 4fp0 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41304.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% (w/v) PEG1500, 120mM glycine, 70mM KNO3, 100mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12706 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→50 Å / Num. all: 107402 / Num. obs: 107280 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.68→1.71 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.5 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2MNR Resolution: 1.68→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.329 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 16.525 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.724 Å / Total num. of bins used: 20
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