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Yorodumi- PDB-1gkp: D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space gr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gkp | ||||||
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Title | D-Hydantoinase (Dihydropyrimidinase) from Thermus sp. in space group C2221 | ||||||
Components | HYDANTOINASE | ||||||
Keywords | HYDROLASE / HYDANTOINASE / DIHYDROPYRIMIDINASE / CYCLIC AMIDASE | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMUS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.295 Å | ||||||
Authors | Abendroth, J. / Niefind, K. / Schomburg, D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: X-Ray Structure of a Dihydropyrimidinase from Thermus Sp. At 1.3 A Resolution Authors: Abendroth, J. / Niefind, K. / Schomburg, D. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization, Preliminary X-Ray Analysis of a Native and Selenomethionine D-Hydantoinase from Thermus Sp 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gkp.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1gkp.ent.gz | 1023.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gkp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gkp ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gkp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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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.: 6 Source method: isolated from a genetically manipulated source Details: KCX IS A NZ-CARBOXYLATED LYSINE / Source: (gene. exp.) THERMUS SP. (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q7SIE9*PLUS, dihydropyrimidinase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 41 % Description: MAD DATA TO 3AA, INITIAL MODEL FROM ARP AT 1.7AA | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 1.65 MM AMMONIUM SULPHATE, 100 MM HEPES/NAOH PH 7.5, 5% (V/V) PEG 400, CRYO-BUFFER: 2 M LITHIUM SULPHATE, 100 MM HEPES/NAOH PH 7.5, 5% (V/V) PEG 400 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.842 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 24, 2000 |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.842 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 693388 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.4 / % possible all: 98 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. measured all: 2976914 |
Reflection shell | *PLUS % possible obs: 98 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.295→50 Å / SU B: 1.996 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / Details: NONE
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Refinement step | Cycle: LAST / Resolution: 1.295→50 Å
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Refinement | *PLUS Highest resolution: 1.3 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.184 / Rfactor Rwork: 0.153 | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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