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Open data
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Basic information
Entry | Database: PDB / ID: 1nfg | ||||||
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Title | Structure of D-hydantoinase | ||||||
![]() | D-hydantoinase | ||||||
![]() | HYDROLASE / TIM barrel | ||||||
Function / homology | ![]() Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amides / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, Z. / Yang, Y. / Jiang, W. / Arnold, E. / Ding, J. | ||||||
![]() | ![]() Title: Crystal Structure of D-Hydantoinase from Burkholderia pickettii at a Resolution of 2.7 Angstroms: Insights into the Molecular Basis of Enzyme Thermostability. Authors: Xu, Z. / Liu, Y. / Yang, Y. / Jiang, W. / Arnold, E. / Ding, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 358.9 KB | Display | ![]() |
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PDB format | ![]() | 293.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.6 KB | Display | ![]() |
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Full document | ![]() | 533.5 KB | Display | |
Data in XML | ![]() | 77 KB | Display | |
Data in CIF | ![]() | 104 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gkqS 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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Unit cell |
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Components
#1: Protein | Mass: 50039.809 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.36 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 16% PEG6000, 0.1M Bicine, 0.005M CdCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 11, 2002 / Details: confocal mirror |
Radiation | Monochromator: Confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→15 Å / Num. all: 139372 / Num. obs: 53883 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 47.2 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.7→2.79 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 3 / Num. unique all: 5481 / % possible all: 96.8 |
Reflection | *PLUS Highest resolution: 2.7 Å / Num. measured all: 139372 |
Reflection shell | *PLUS Lowest resolution: 2.78 Å / % possible obs: 96.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GKQ Resolution: 2.7→14.94 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 32.0895 Å2 / ksol: 1.4629 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→14.94 Å
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Refine LS restraints |
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LS refinement shell |
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 15 Å / Rfactor Rwork: 0.22 | |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.78 Å / Rfactor Rfree: 0.324 / Num. reflection Rfree: 221 / Rfactor Rwork: 0.303 / Num. reflection obs: 4281 |