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- PDB-4yp7: Crystal structure of Methanobacterium thermoautotrophicum NMNAT i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yp7 | ||||||
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Title | Crystal structure of Methanobacterium thermoautotrophicum NMNAT in complex with NADP | ||||||
![]() | Nicotinamide-nucleotide adenylyltransferase | ||||||
![]() | TRANSFERASE / inhibitor | ||||||
Function / homology | ![]() nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pfoh, R. / Christendat, D. / Pai, E.F. / Saridakis, V. | ||||||
![]() | ![]() Title: Nicotinamide mononucleotide adenylyltransferase displays alternate binding modes for nicotinamide nucleotides. Authors: Pfoh, R. / Pai, E.F. / Saridakis, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 119 KB | Display | ![]() |
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PDB format | ![]() | 91.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yp5C ![]() 4yp6C ![]() 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 20536.648 Da / Num. of mol.: 3 / Mutation: R47E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: MTH_150 / Plasmid: pET15B / Production host: ![]() ![]() References: UniProt: O26253, nicotinamide-nucleotide adenylyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: ammonium sulfate, glycerol, TRIS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→14.99 Å / Num. obs: 41867 / % possible obs: 93.1 % / Redundancy: 1.56 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 1.58 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 6.09 / % possible all: 93.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EJ2 Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2112 / WRfactor Rwork: 0.1982 / FOM work R set: 0.872 / SU B: 4.29 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1997 / SU Rfree: 0.1646 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.12 Å2 / Biso mean: 26.88 Å2 / Biso min: 12.71 Å2
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Refinement step | Cycle: final / Resolution: 2.3→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.299→2.358 Å / Total num. of bins used: 20
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