[English] 日本語
Yorodumi- PDB-5das: Structure of Mycobacterium tuberculosis NadD in complex with NADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5das | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212, form 2 | ||||||||||||
Components | Nicotinate-nucleotide adenylyltransferase | ||||||||||||
Keywords | TRANSFERASE / Rossman fold | ||||||||||||
Function / homology | Function and homology information nicotinate-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||||||||
Authors | Korotkov, K.V. | ||||||||||||
Funding support | United States, 3items
| ||||||||||||
Citation | Journal: to be published Title: Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212 Authors: Korotkov, K.V. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5das.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5das.ent.gz | 130.4 KB | Display | PDB format |
PDBx/mmJSON format | 5das.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/5das ftp://data.pdbj.org/pub/pdb/validation_reports/da/5das | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ybrC 4s1oS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22352.281 Da / Num. of mol.: 4 / Fragment: Residues 1-192 / Mutation: C188R, C192T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: nadD, Rv2421c, MTCY428.26 / Plasmid: pRSF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P9WJJ5, nicotinate-nucleotide adenylyltransferase #2: Chemical | ChemComp-NAP / #3: Water | ChemComp-HOH / | Sequence details | THE AUTHORS STATE THAT THE SEQUENCE IS MIS-ANNOTATED IN THE DATABASES. THE CORRECT START SEQUENCE ...THE AUTHORS STATE THAT THE SEQUENCE IS MIS-ANNOTATED IN THE DATABASES. THE CORRECT START SEQUENCE IS MHGRRLGVM WHICH WAS CONFIRMED EXPERIMENT | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.15 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M sodium citrate pH 5.6, 20% isopropanol, 20% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97903 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 4, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→65.08 Å / Num. obs: 46782 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 29.1 Å2 / Rmerge F obs: 0.99 / Rmerge(I) obs: 0.209 / Rrim(I) all: 0.227 / Χ2: 0.955 / Net I/σ(I): 7.97 / Num. measured all: 304725 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4S1O Resolution: 2.2→65.08 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2274 / WRfactor Rwork: 0.1839 / FOM work R set: 0.82 / SU B: 6.081 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2438 / SU Rfree: 0.1996 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.54 Å2 / Biso mean: 27.274 Å2 / Biso min: 6.74 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→65.08 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
|