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- PDB-3uxk: P. putida mandelate racemase co-crystallized with the intermediat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3uxk | ||||||
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Title | P. putida mandelate racemase co-crystallized with the intermediate analogue benzohydroxamate | ||||||
![]() | Mandelate racemase | ||||||
![]() | ISOMERASE / Enolase superfamily enzyme | ||||||
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. / Pellmann, E. / St Maurice, M. | ||||||
![]() | ![]() Title: Structure of mandelate racemase with bound intermediate analogues benzohydroxamate and cupferron. Authors: Lietzan, A.D. / Nagar, M. / Pellmann, E.A. / Bourque, J.R. / Bearne, S.L. / St Maurice, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 289.6 KB | Display | ![]() |
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PDB format | ![]() | 232.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3uxlC ![]() 2mnrS C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41304.621 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-BHO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 14% (w/v) PEG1500, 200mM glycine, 50mM NaI, 100mM Triethanolamine 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 225 mm CCD / Detector: CCD / Date: Oct 18, 2010 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 92408 / Num. obs: 92311 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 28 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 8.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2MNR Resolution: 2.201→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.58 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.157 / 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: 17.361 Å2
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Refinement step | Cycle: LAST / Resolution: 2.201→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.201→2.258 Å / Total num. of bins used: 20
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