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Yorodumi- PDB-1k4m: Crystal structure of E.coli nicotinic acid mononucleotide adenyly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k4m | ||||||
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Title | Crystal structure of E.coli nicotinic acid mononucleotide adenylyltransferase complexed to deamido-NAD | ||||||
Components | NaMN adenylyltransferase | ||||||
Keywords | TRANSFERASE / Nucleotidyltransferase | ||||||
Function / homology | Function and homology information NAD salvage / 'de novo' NAD biosynthetic process from aspartate / nicotinate-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Zhang, H. / Zhou, T. / Kurnasov, O. / Cheek, S. / Grishin, N.V. / Osterman, A. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD. Authors: Zhang, H. / Zhou, T. / Kurnasov, O. / Cheek, S. / Grishin, N.V. / Osterman, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k4m.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k4m.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 1k4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k4m_validation.pdf.gz | 616.6 KB | Display | wwPDB validaton report |
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Full document | 1k4m_full_validation.pdf.gz | 641.3 KB | Display | |
Data in XML | 1k4m_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1k4m_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/1k4m ftp://data.pdbj.org/pub/pdb/validation_reports/k4/1k4m | HTTPS FTP |
-Related structure data
Related structure data | 1k4kSC S: Starting model for refinement C: citing same article (ref.) |
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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 biological unit of the protein is monomer |
-Components
#1: Protein | Mass: 24553.871 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NADD / Production host: Escherichia coli (E. coli) References: UniProt: P0A752, nicotinate-nucleotide adenylyltransferase #2: Chemical | #3: Chemical | #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: 2.57 Å3/Da / Density % sol: 52.06 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: Na citrate, NaCl, Tris, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 5, 2001 / Details: Osmic mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 59943 / Num. obs: 57802 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. measured all: 180068 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 67.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1k4k Resolution: 1.9→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refinement | *PLUS Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor obs: 0.206 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.206 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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