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Yorodumi- PDB-1ilw: Crystal Structure of Pyrazinamidase/Nicotinamidase of Pyrococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ilw | ||||||
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Title | Crystal Structure of Pyrazinamidase/Nicotinamidase of Pyrococcus horikoshii | ||||||
Components | 180 aa long hypothetical Pyrazinamidase/nicotinamidase | ||||||
Keywords | HYDROLASE / Pyrazinamide / pyrazinamidase / nicotinamidase / tuberculosis / cysteine hydrolase / amidase / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center | ||||||
Function / homology | Function and homology information pyridine nucleotide biosynthetic process / nicotinamidase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Du, X. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC) | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Crystal structure and mechanism of catalysis of a pyrazinamidase from Pyrococcus horikoshii. Authors: Du, X. / Wang, W. / Kim, R. / Yakota, H. / Nguyen, H. / Kim, S.-H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ilw.cif.gz | 49 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ilw.ent.gz | 34.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ilw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/1ilw ftp://data.pdbj.org/pub/pdb/validation_reports/il/1ilw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20222.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)/SJS1244 / References: UniProt: O58727, nicotinamidase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.46 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 22.5% PEG3350, 250 mM ammonium acetate, 100 mM sodium acetate, pH 4.6. Seeding., VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. all: 9941 / Num. obs: 9862 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.246 % / Biso Wilson estimate: 6.2 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 42.5 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 17.4 / % possible all: 88 |
Reflection | *PLUS Rmerge(I) obs: 0.027 |
Reflection shell | *PLUS % possible obs: 88 % / Rmerge(I) obs: 0.093 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: a structure of the same protein obtained on MAD data Resolution: 2.05→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 899942.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh $ Huber
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Displacement parameters | Biso mean: 23.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 9761 / σ(F): 0 / Num. reflection Rfree: 955 / Rfactor obs: 0.181 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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