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Yorodumi- PDB-1f9a: CRYSTAL STRUCTURE ANALYSIS OF NMN ADENYLYLTRANSFERASE FROM METHAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f9a | ||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF NMN ADENYLYLTRANSFERASE FROM METHANOCOCCUS JANNASCHII | ||||||
Components | HYPOTHETICAL PROTEIN MJ0541 | ||||||
Keywords | TRANSFERASE / alpha/beta / HYPOTHETICAL PROTEIN / STRUCTURAL GENOMICS | ||||||
Function / homology | Function and homology information nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2 Å | ||||||
Authors | D'Angelo, I. / Raffaelli, N. / Dabusti, V. / Lorenzi, T. / Magni, G. / Rizzi, M. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Structure of nicotinamide mononucleotide adenylyltransferase: a key enzyme in NAD(+) biosynthesis. Authors: D'Angelo, I. / Raffaelli, N. / Dabusti, V. / Lorenzi, T. / Magni, G. / Rizzi, M. #1: Journal: J.Bacteriol. / Year: 1997 Title: Characterization of nicotinamide mononucleotide adenylyltransferase from Thermophilic archaea Authors: Raffaelli, N. / Pisani, F.M. / Lorenzi, T. / Emanuelli, M. / Amici, A. / Ruggieri, S. / Magni, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f9a.cif.gz | 230.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f9a.ent.gz | 184.7 KB | Display | PDB format |
PDBx/mmJSON format | 1f9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f9a_validation.pdf.gz | 784 KB | Display | wwPDB validaton report |
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Full document | 1f9a_full_validation.pdf.gz | 847.7 KB | Display | |
Data in XML | 1f9a_validation.xml.gz | 31.8 KB | Display | |
Data in CIF | 1f9a_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/1f9a ftp://data.pdbj.org/pub/pdb/validation_reports/f9/1f9a | 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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Unit cell |
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Details | The asymmetric unit contains and homohexamer having 32 point group symmetry |
-Components
#1: Protein | Mass: 19621.697 Da / Num. of mol.: 6 / Fragment: NMN ADENYLYLTRANSFERASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q57961 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-ATP / #4: 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: 2.54 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Jeffamine M600, Hepes, cesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
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: 0.8139 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8139 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 200580 / Num. obs: 80232 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2→20 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.178 / Num. unique all: 11668 / % possible all: 95.6 |
Reflection | *PLUS % possible obs: 96 % / Num. measured all: 200580 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber / Details: Used maximum likelihood procedure
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Displacement parameters | Biso mean: 36.5 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 36.5 Å2 |