+Open data
-Basic information
Entry | Database: PDB / ID: 1k1d | ||||||
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Title | Crystal structure of D-hydantoinase | ||||||
Components | D-hydantoinase | ||||||
Keywords | HYDROLASE / D-hydantoinase | ||||||
Function / homology | Function and homology information 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 | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Cheon, Y.H. / Kim, H.S. / Han, K.H. / Abendroth, J. / Niefind, K. / Schomburg, D. / Wang, J. / Kim, Y. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal structure of D-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity. Authors: Cheon, Y.H. / Kim, H.S. / Han, K.H. / Abendroth, J. / Niefind, K. / Schomburg, D. / Wang, J. / Kim, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k1d.cif.gz | 674.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k1d.ent.gz | 579.7 KB | Display | PDB format |
PDBx/mmJSON format | 1k1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k1d_validation.pdf.gz | 515.3 KB | Display | wwPDB validaton report |
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Full document | 1k1d_full_validation.pdf.gz | 676.3 KB | Display | |
Data in XML | 1k1d_validation.xml.gz | 142.7 KB | Display | |
Data in CIF | 1k1d_validation.cif.gz | 191 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/1k1d ftp://data.pdbj.org/pub/pdb/validation_reports/k1/1k1d | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-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: 50633.621 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: pMAL-c2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45515 #2: Chemical | ChemComp-ZN / |
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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: 3.08 Å3/Da / Density % sol: 60.12 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 125 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.91 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jan 7, 2001 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. all: 96278 / Num. obs: 96187 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.74 |
Reflection shell | Resolution: 3→3.11 Å / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 943917 / Rmerge(I) obs: 0.138 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→19.97 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 60706.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.4953 Å2 / ksol: 0.341808 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.01→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor obs: 0.263 / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.263 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.431 / Rfactor Rwork: 0.401 |