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Open data
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Basic information
Entry | Database: PDB / ID: 1gkr | ||||||
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Title | L-Hydantoinase (Dihydropyrimidinase) from Arthrobacter aurescens | ||||||
![]() | NON-ATP DEPENDENT L-SELECTIVE HYDANTOINASE | ||||||
![]() | HYDROLASE / HYDANTOINASE / DIHYDROPYRIMIDINASE / CYCLIC AMIDASE | ||||||
Function / homology | ![]() Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amides / allantoinase activity / allantoin catabolic process / cobalt ion binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Abendroth, J. / Niefind, K. / Schomburg, D. | ||||||
![]() | ![]() Title: The structure of L-hydantoinase from Arthobacter aurescens leads to an understanding of dihydropyrimidinase substrate and enantio specificity. Authors: Abendroth, J. / Niefind, K. / May, O. / Siemann, M. / Syldatk, C. / Schomburg, D. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Crystallization and Preliminary X-Ray Analysis of a Hydantoinase from Arthrobacter Aurescens Dsm 3745. Authors: May, O. / Siemann, M. / Syldatk, C. / 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 | ![]() | 351 KB | Display | ![]() |
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PDB format | ![]() | 287.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.4 KB | Display | ![]() |
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Full document | ![]() | 526.7 KB | Display | |
Data in XML | ![]() | 74.7 KB | Display | |
Data in CIF | ![]() | 101.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gkpS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 49693.445 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: DSM 3745 / Source: (natural) ![]() #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: 1.2 Å3/Da / Density % sol: 63 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 16-18% (W/V) PEG 8000, 250 MM LITHIUM SULPHATE, 100 MM MES/TRIS PH 8.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 292 K / pH: 8 / Method: vapor diffusion, sitting dropDetails: May, O., (1996) Acta Crystallogr.,Sect.D, D52, 1209. | |||||||||||||||||||||||||||||||||||||||||||||||||
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: SIEMENS / Detector: AREA DETECTOR / Date: Mar 20, 1996 |
Radiation | Monochromator: GRAPHITE CRYSTAL / 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→20 Å / Num. obs: 61763 / % possible obs: 86.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.148 / Mean I/σ(I) obs: 2.5 / % possible all: 41.2 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Num. measured all: 124261 |
Reflection shell | *PLUS % possible obs: 41.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HOMOLOGY MODEL FROM PDB ENTRY 1GKP Resolution: 2.6→30 Å / Rfactor Rfree error: 0.0043 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE STRUCTURE HAS BEEN REFINED WITH ONLY ONE CHAIN USING THE NCS MATRICES GIVEN BELOW
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Solvent computation | Bsol: 30.7 Å2 / ksol: 0.295 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.69 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 10
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Refinement | *PLUS Lowest resolution: 30 Å / Rfactor Rfree: 0.243 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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