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- PDB-2f7f: Crystal structure of Enterococcus faecalis putative nicotinate ph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f7f | ||||||
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Title | Crystal structure of Enterococcus faecalis putative nicotinate phosphoribosyltransferase, NEW YORK STRUCTURAL GENOMICS CONSORTIUM | ||||||
![]() | nicotinate phosphoribosyltransferase, putative![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal Structure of Enterococcus Faecalis Nicotinate Phosphoribosyltransferase Authors: Patskovsky, Y. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.2 KB | Display | ![]() |
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PDB format | ![]() | 92.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4mzyC ![]() 1ytdS S: Starting model for refinement C: citing same article ( |
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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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Unit cell |
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Components on special symmetry positions |
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Details | Homodimer. The second part of the biological assembly is generated by the two fold axis: -x, -y, z. |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | ![]() Mass: 56600.828 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 402 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/NIO.gif)
![](data/chem/img/DPO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NIO.gif)
![](data/chem/img/DPO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-DPO / | ![]() #5: Chemical | ChemComp-GOL / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 49.73 % |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100 mM HEPES, 2 M AMMONIUM SULFATE, 10% GLYCEROL, PH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 8, 2005 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→50 Å / Num. all: 41720 / Num. obs: 41577 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.066 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4095 / Rsym value: 0.66 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1YTD Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.821 / SU ML: 0.106 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.153 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.365 Å2
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Refine analyze | Luzzati coordinate error free: 0.087 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 20
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