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Yorodumi- PDB-1k4k: Crystal structure of E. coli Nicotinic acid mononucleotide adenyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k4k | ||||||
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Title | Crystal structure of E. coli Nicotinic acid mononucleotide adenylyltransferase | ||||||
Components | Nicotinic acid mononucleotide 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 / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Zhang, H. / Zhou, T. / Kurnasov, O. / Cheek, S. / Grishin, N.V. / Osterman, A.L. | ||||||
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 | 1k4k.cif.gz | 188.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k4k.ent.gz | 151.1 KB | Display | PDB format |
PDBx/mmJSON format | 1k4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/1k4k ftp://data.pdbj.org/pub/pdb/validation_reports/k4/1k4k | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | The functional unit of this protein is monomer. |
-Components
#1: Protein | Mass: 24553.871 Da / Num. of mol.: 4 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 | ChemComp-XE / #3: 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: 52.07 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Na Citrate, sodium chloride, Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2→40 Å / Num. all: 66058 / Num. obs: 62463 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.9 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4 / % possible all: 81.9 | ||||||||||||||||||
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 169804 / Rmerge(I) obs: 0.045 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 81.9 % / Rmerge(I) obs: 0.25 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: o_angle_deg / Dev ideal: 1.7 |