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Yorodumi- PDB-4rpi: Crystal Structure of Nicotinate Mononucleotide Adenylyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rpi | ||||||
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Title | Crystal Structure of Nicotinate Mononucleotide Adenylyltransferase from Mycobacterium tuberculosis | ||||||
Components | nicotinate-nucleotide adenylyltransferase | ||||||
Keywords | TRANSFERASE / NadD / NAD biosynthesis | ||||||
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 / Resolution: 2.417 Å | ||||||
Authors | Rodionova, I. / Zuccola, H. / Sorci, L. / Aleshin, A.E. / Kazanov, M. / Sergienko, E. / Rubin, E. / Locher, C. / Osterman, A. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2015 Title: Mycobacterial nicotinate mononucleotide adenylyltransferase: structure, mechanism, and implications for drug discovery. Authors: Rodionova, I.A. / Zuccola, H.J. / Sorci, L. / Aleshin, A.E. / Kazanov, M.D. / Ma, C.T. / Sergienko, E. / Rubin, E.J. / Locher, C.P. / Osterman, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rpi.cif.gz | 164.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rpi.ent.gz | 132.4 KB | Display | PDB format |
PDBx/mmJSON format | 4rpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rpi_validation.pdf.gz | 485.6 KB | Display | wwPDB validaton report |
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Full document | 4rpi_full_validation.pdf.gz | 491.6 KB | Display | |
Data in XML | 4rpi_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 4rpi_validation.cif.gz | 41.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rp/4rpi ftp://data.pdbj.org/pub/pdb/validation_reports/rp/4rpi | HTTPS FTP |
-Related structure data
-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: 24187.338 Da / Num. of mol.: 4 / Mutation: W117A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: nadD, HKBS1_2563 / Plasmid: pODC29 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: W6GSY1, UniProt: P9WJJ5*PLUS, nicotinate-nucleotide adenylyltransferase #2: Chemical | ChemComp-EPE / #3: Chemical | ChemComp-DMS / #4: 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: 2.2 Å3/Da / Density % sol: 44.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 7 mg/ml protein in 150 mM sodium chloride, 20 mM Tris, pH 8.0, 2.5% v/v DMSO, 0.7 mM TCEP mixed 1:1 with 25% PEG3350, 0.1 M HEPES, 0.2 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 160 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2014 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.417→34 Å / Num. all: 34307 / Num. obs: 32648 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.417→2.51 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.6 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.417→33.831 Å / SU ML: 0.32 / σ(F): 1.2 / Phase error: 30.89 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.417→33.831 Å
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Refine LS restraints |
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LS refinement shell |
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