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- PDB-1gkq: D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space gr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gkq | ||||||
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Title | D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space group P212121 | ||||||
![]() | HYDANTOINASE | ||||||
![]() | HYDROLASE / HYDANTOINASE / DIHYDROPYRIMIDINASE / CYCLIC AMIDASE | ||||||
Function / homology | ![]() hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Abendroth, J. / Niefind, K. / Schomburg, D. | ||||||
![]() | ![]() Title: X-Ray Structure of a Dihydropyrimidinase from Thermus Sp. At 1.3 A Resolution Authors: Abendroth, J. / Niefind, K. / Schomburg, D. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 365.2 KB | Display | ![]() |
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PDB format | ![]() | 299 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459 KB | Display | ![]() |
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Full document | ![]() | 474 KB | Display | |
Data in XML | ![]() | 68 KB | Display | |
Data in CIF | ![]() | 94 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gkpSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 50781.422 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: KCX IS A NZ-CARBOXYLATED LYSINE / 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: 2.8 Å3/Da / Density % sol: 61 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 30% (W/V) PEG 6000, 100 MM CACODYLATE/HCL PH 6.5, 200 MM SODIUM ACETATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAC SCIENCE DIP-2030H / Detector: IMAGE PLATE / Date: Nov 6, 1997 |
Radiation | Monochromator: NI FITER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. obs: 70394 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.9 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 25 Å / % possible obs: 99.9 % / Num. measured all: 416020 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GKP Resolution: 2.6→25 Å / Rfactor Rfree error: 0.0035 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 42.4 Å2 / ksol: 0.355 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev position: 300 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
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Refinement | *PLUS Rfactor Rfree: 0.211 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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