+Open data
-Basic information
Entry | Database: PDB / ID: 2pzb | ||||||
---|---|---|---|---|---|---|---|
Title | NAD+ Synthetase from Bacillus anthracis | ||||||
Components | NH(3)-dependent NAD(+) synthetase | ||||||
Keywords | LIGASE / NAD+ synthetase / His-tag / Bacillus anthracis | ||||||
Function / homology | Function and homology information NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | McDonald, H.M. / Pruett, P.S. / Deivanayagam, C. / Protasevich, I.I. / Carson, W.M. / DeLucas, L.J. / Brouillette, W.J. / Brouillette, C.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Structural adaptation of an interacting non-native C-terminal helical extension revealed in the crystal structure of NAD(+) synthetase from Bacillus anthracis. Authors: McDonald, H.M. / Pruett, P.S. / Deivanayagam, C. / Protasevich, I.I. / Carson, W.M. / DeLucas, L.J. / Brouillette, W.J. / Brouillette, C.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2pzb.cif.gz | 212.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2pzb.ent.gz | 170.9 KB | Display | PDB format |
PDBx/mmJSON format | 2pzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/2pzb ftp://data.pdbj.org/pub/pdb/validation_reports/pz/2pzb | HTTPS FTP |
---|
-Related structure data
Related structure data | 2pz8C 2pzaC 1ee1S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The functional unit of the enzyme is a homodimer. |
-Components
#1: Protein | Mass: 31534.582 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: nadE / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q81RP3, NAD+ synthase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.56 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% PEG 8000, 0.505 M ammonium sulfate, 6% glycerol, 100 mM MgCl2, 0.05% n-octyl-BETA-D-glucopyranoside, 100 mM HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→36.1 Å / Num. all: 138893 / Num. obs: 131948 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.24 % / Biso Wilson estimate: 24.5 Å2 / Rsym value: 0.63 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.22 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 13773 / Rsym value: 0.281 / % possible all: 90.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Swiss Model of B. anthracis NAD+ synthetase derived from PDB ENTRY 1EE1 Resolution: 1.9→36.1 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 602000.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.9533 Å2 / ksol: 0.382959 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.2 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→36.1 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|