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Yorodumi- PDB-1m8j: Crystal Structure Of Methanobacterium Thermoautotrophicum Nicotin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1m8j | ||||||
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Title | Crystal Structure Of Methanobacterium Thermoautotrophicum Nicotinamide Mononucleotide Adenylyltransferase Mutant R136A complexed with NAD | ||||||
Components | Nicotinamide-nucleotide Adenylyltransferase | ||||||
Keywords | TRANSFERASE / nucleotidyltransferase HXGH active site motif | ||||||
Function / homology | Function and homology information nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Saridakis, V. / Pai, E.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1m8j.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1m8j.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 1m8j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m8j_validation.pdf.gz | 476.2 KB | Display | wwPDB validaton report |
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Full document | 1m8j_full_validation.pdf.gz | 479.3 KB | Display | |
Data in XML | 1m8j_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1m8j_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/1m8j ftp://data.pdbj.org/pub/pdb/validation_reports/m8/1m8j | HTTPS FTP |
-Related structure data
Related structure data | 1m8fC 1m8gC 1m8kC 1ej2S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The protein is hexameric. |
-Components
#1: Protein | Mass: 20478.613 Da / Num. of mol.: 1 / Mutation: R136A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: mth0150 / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O26253, nicotinamide-nucleotide adenylyltransferase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-NAD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 10961 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 29.5 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.094 / Net I/σ(I): 49.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 15 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 13.4 / Num. unique all: 1052 / Rsym value: 0.345 |
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 10085 / % possible obs: 99.8 % / Num. measured all: 185814 / Rmerge(I) obs: 0.077 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 12 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1ej2 Resolution: 2.4→14.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 521275.62 / Data cutoff high rms absF: 521275.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.833 Å2 / ksol: 0.376268 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→14.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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