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Yorodumi- PDB-1im5: Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1im5 | ||||||
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Title | Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc | ||||||
Components | 180aa long hypothetical Pyrazinamidase/Nicotinamidase | ||||||
Keywords | HYDROLASE / pyrazinamidase / pyrazinamide / nicotinamidase / tuberculosis / PZA resistance / drug resistance / metal ion catalysis / cysteine hydrolase / amidase / covalent catalysis | ||||||
Function / homology | Function and homology information pyridine nucleotide biosynthetic process / nicotinamidase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Du, X. / Kim, S.-H. | ||||||
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 | 1im5.cif.gz | 90.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1im5.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 1im5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1im5_validation.pdf.gz | 428.8 KB | Display | wwPDB validaton report |
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Full document | 1im5_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 1im5_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1im5_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/1im5 ftp://data.pdbj.org/pub/pdb/validation_reports/im/1im5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | monomer is biologically active |
-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) / Gene: PH 999 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)/SJS1244 / References: UniProt: O58727, nicotinamidase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal |
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Crystal grow |
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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: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 24, 2000 / Details: mirrors |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. all: 18550 / Num. obs: 18049 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.11 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 37.8 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 2.02 % / Rmerge(I) obs: 0.064 / Mean I/σ(I) obs: 25.5 / Num. unique all: 753 / % possible all: 81.9 |
Reflection shell | *PLUS % possible obs: 81.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: a structure obtained on MAD data Resolution: 1.65→20 Å / Num. parameters: 14202 / Num. restraintsaints: 17019 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1552 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.6 % / Rfactor all: 0.153 / Rfactor Rfree: 0.232 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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