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Yorodumi- PDB-2qtn: Crystal Structure of Nicotinate Mononucleotide Adenylyltransferase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qtn | ||||||
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Title | Crystal Structure of Nicotinate Mononucleotide Adenylyltransferase | ||||||
Components | Nicotinate (Nicotinamide) nucleotide adenylyltransferase | ||||||
Keywords | TRANSFERASE / NAD / Nucleotidyltransferase / Pyridine nucleotide biosynthesis | ||||||
Function / homology | HUPs / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINATE MONONUCLEOTIDE / : Function and homology information | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Sershon, V.C. / Santarsiero, B.D. / Mesecar, A.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Kinetic and X-ray structural evidence for negative cooperativity in substrate binding to nicotinate mononucleotide adenylyltransferase (NMAT) from Bacillus anthracis. Authors: Sershon, V.C. / Santarsiero, B.D. / Mesecar, A.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qtn.cif.gz | 94 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qtn.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qtn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/2qtn ftp://data.pdbj.org/pub/pdb/validation_reports/qt/2qtn | HTTPS FTP |
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-Related structure data
Related structure data | 2qtmC 2qtrC 1kaqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | BIOLOGICAL UNIT IS A DIMER AND THE SAME AS IN ASYMMETRIC UNIT |
-Components
#1: Protein | Mass: 21983.305 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: sterne / Gene: NadD / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)3 References: UniProt: Q6HT60, nicotinate-nucleotide adenylyltransferase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NCN / | #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: 2.55 Å3/Da / Density % sol: 51.8 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.2 Details: sodium chloride, glycerol, tacismate, cobalt chloride, nicotinic acid mononculeotide, pH 7.2, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 16503 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.086 / Χ2: 1.792 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2 % / Rmerge(I) obs: 0.973 / Num. unique all: 1145 / Χ2: 1.352 / % possible all: 66.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KAQ Resolution: 2.4→20 Å / FOM work R set: 0.773 / σ(F): 0
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Solvent computation | Bsol: 57.488 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.158 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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Xplor file |
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