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Open data
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Basic information
Entry | Database: PDB / ID: 1yir | ||||||
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Title | Crystal Structure of a Nicotinate Phosphoribosyltransferase | ||||||
![]() | Nicotinate phosphoribosyltransferase 2 | ||||||
![]() | TRANSFERASE / Structural genomics / Protein structure initiative / Hypothetical protein / NYSGXRC / T1804 / PSI / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | ![]() nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase activity / NAD salvage / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seetharaman, J. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal Structure of a Nicotinate Phosphoribosyltransferase Authors: Seetharaman, J. / Swaminathan, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 330.4 KB | Display | ![]() |
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PDB format | ![]() | 268.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479 KB | Display | ![]() |
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Full document | ![]() | 514.6 KB | Display | |
Data in XML | ![]() | 64.8 KB | Display | |
Data in CIF | ![]() | 90.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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Links
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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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Components
#1: Protein | Mass: 46964.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Ammonium Sulphate, PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2004 / Details: mirrors | ||||||||||||
Radiation | Monochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→50 Å / Num. all: 129962 / Num. obs: 129962 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2 | ||||||||||||
Reflection shell | Resolution: 2→2.18 Å / % possible all: 97.9 |
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Processing
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Refinement | Method to determine structure: ![]() Details: The atoms listed in remark 470 are missing due to lack of electron density.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.0647 Å2 / ksol: 0.355384 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→48.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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