+Open data
-Basic information
Entry | Database: PDB / ID: 1lqu | ||||||
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Title | Mycobacterium tuberculosis FprA in complex with NADPH | ||||||
Components | FprAFlorida Public Relations Association | ||||||
Keywords | OXIDOREDUCTASE / tuberculosis / NADPH / FAD / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information ferredoxin-NAD+ reductase activity / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADP+ binding / peptidoglycan-based cell wall / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.25 Å | ||||||
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. ...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) | ||||||
Citation | Journal: Biochemistry / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lqu.cif.gz | 627.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lqu.ent.gz | 527.6 KB | Display | PDB format |
PDBx/mmJSON format | 1lqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/1lqu ftp://data.pdbj.org/pub/pdb/validation_reports/lq/1lqu | HTTPS FTP |
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-Related structure data
Related structure data | 1lqtC 1qltS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-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.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O05783, UniProt: P9WIQ3*PLUS #2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | #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: 2.54 Å3/Da / Density % sol: 51.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 Å |
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: 1.25→20 Å / Num. all: 275836 / Num. obs: 275836 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.25→1.31 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.5 / Num. unique all: 38255 / Rsym value: 0.304 / % possible all: 93.8 |
Reflection | *PLUS Num. measured all: 877990 |
Reflection shell | *PLUS % possible obs: 98.1 % |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1QLT Resolution: 1.25→40 Å / Cor.coef. Fo:Fc: 0.981 / SU B: 1.076 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.033 / 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: 12.756 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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Refinement | *PLUS % reflection Rfree: 0.5 % / Rfactor Rwork: 0.125 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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