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- PDB-1lqt: A covalent modification of NADP+ revealed by the atomic resolutio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1lqt | ||||||
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Title | A covalent modification of NADP+ revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase | ||||||
![]() | FprA | ||||||
![]() | OXIDOREDUCTASE / NADP+ derivative / tuberculosis / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | ![]() NADPH-adrenodoxin reductase activity / ferredoxin-NAD+ reductase activity / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / ubiquinone biosynthetic process / NADP+ binding / peptidoglycan-based cell wall / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bossi, R.T. / Aliverti, A. / Raimondi, D. / Fischer, F. / Zanetti, G. / Ferrari, D. / Tahallah, N. / Maier, C.S. / Heck, A.J.R. / Rizzi, M. ...Bossi, R.T. / Aliverti, A. / Raimondi, D. / Fischer, F. / Zanetti, G. / Ferrari, D. / Tahallah, N. / Maier, C.S. / Heck, A.J.R. / Rizzi, M. / Mattevi, A. / TB Structural Genomics Consortium (TBSGC) | ||||||
![]() | ![]() Title: A covalent modification of NADP+ revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase. Authors: Bossi, R.T. / Aliverti, A. / Raimondi, D. / Fischer, F. / Zanetti, G. / Ferrari, D. / Tahallah, N. / Maier, C.S. / Heck, A.J.R. / Rizzi, M. / Mattevi, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 668.1 KB | Display | ![]() |
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PDB format | ![]() | 564.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 56.6 KB | Display | |
Data in CIF | ![]() | 90.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lquC ![]() 1e1lS C: citing same article ( S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49403.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 31, 2001 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→20 Å / Num. all: 440216 / Num. obs: 440216 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 1.05→1.11 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 62782 / Rsym value: 0.485 / % possible all: 93.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 1170509 |
Reflection shell | *PLUS % possible obs: 95.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1E1L Resolution: 1.05→40 Å / Cor.coef. Fo:Fc: 0.983 / SU B: 0.756 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.815 Å2
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Refinement step | Cycle: LAST / Resolution: 1.05→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Total num. of bins used: 20
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Refinement | *PLUS % reflection Rfree: 0.5 % / Rfactor Rwork: 0.134 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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