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- PDB-1m8f: Crystal Structure Of Methanobacterium Thermoautotrophicum Nicotin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1m8f | ||||||
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Title | Crystal Structure Of Methanobacterium Thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase Mutant R11A complexed with NAD | ||||||
![]() | nicotinamide-nucleotide adenylyltransferase | ||||||
![]() | TRANSFERASE / nucleotidyltransferase HXGH motif | ||||||
Function / homology | ![]() nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Saridakis, V. / Pai, E.F. | ||||||
![]() | ![]() Title: Mutational, Structural, and Kinetic Studies of the ATP-binding Site of Methanobacterium thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase Authors: Saridakis, V. / Pai, E.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.8 KB | Display | ![]() |
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PDB format | ![]() | 35.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 466 KB | Display | ![]() |
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Full document | ![]() | 469.2 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m8gC ![]() 1m8jC ![]() 1m8kC ![]() 1ej2S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The biologically active protein is hexameric |
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Components
#1: Protein | Mass: 20478.613 Da / Num. of mol.: 1 / Mutation: R11A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: mth150 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: ![]() ![]() References: UniProt: O26253, nicotinamide-nucleotide adenylyltransferase |
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#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.47 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.5 M Ammonium Sulfate, 100 mM Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 9715 / Num. obs: 9266 / % possible obs: 88.4 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.058 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.5 / Num. unique all: 978 / Rsym value: 0.45 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 9715 / % possible obs: 92.9 % / Num. measured all: 42952 |
Reflection shell | *PLUS % possible obs: 96.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EJ2 Resolution: 2.4→28.28 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 253779.59 / Data cutoff high rms absF: 253779.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.0349 Å2 / ksol: 0.351916 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→28.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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