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Yorodumi- PDB-2nsy: CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nsy | ||||||
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Title | CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS IN COMPLEX WITH NAD-ADENYLATE | ||||||
Components | PROTEIN (NAD SYNTHETASE) | ||||||
Keywords | LIGASE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP PYROPHOSPHATASE | ||||||
Function / homology | Function and homology information NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / sporulation resulting in formation of a cellular spore / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å | ||||||
Authors | Rizzi, M. / Bolognesi, M. / Coda, A. | ||||||
Citation | Journal: Structure / Year: 1998 Title: A novel deamido-NAD+-binding site revealed by the trapped NAD-adenylate intermediate in the NAD+ synthetase structure. Authors: Rizzi, M. / Bolognesi, M. / Coda, A. #1: Journal: Embo J. / Year: 1996 Title: Crystal Structure of Nh3-Dependent Nad+ Synthetase from Bacillus Subtilis Authors: Rizzi, M. / Nessi, C. / Mattevi, A. / Coda, A. / Bolognesi, M. / Galizzi, A. #2: Journal: J.Biol.Chem. / Year: 1995 Title: The Outb Gene of Bacillus Subtilis Codes for Nad Synthetase Authors: Nessi, C. / Albertini, A.M. / Speranza, M.L. / Galizzi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nsy.cif.gz | 137.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nsy.ent.gz | 105.2 KB | Display | PDB format |
PDBx/mmJSON format | 2nsy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/2nsy ftp://data.pdbj.org/pub/pdb/validation_reports/ns/2nsy | HTTPS FTP |
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-Related structure data
Related structure data | 1nsyS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.60859, 0.72528, -0.32183), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30303.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing) |
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-Non-polymers , 6 types, 505 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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: 2.08 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 / Details: pH 5.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
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: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 7, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→20 Å / Num. obs: 111493 / % possible obs: 92 % / Redundancy: 3 % / Rmerge(I) obs: 0.034 |
Reflection | *PLUS Num. measured all: 333971 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 1NSY Resolution: 2→15 Å / σ(F): 0
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Displacement parameters | Biso mean: 15.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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