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- PDB-1ypf: Crystal Structure of GuaC (BA5705) from Bacillus anthracis at 1.8... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ypf | ||||||
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Title | Crystal Structure of GuaC (BA5705) from Bacillus anthracis at 1.8 A Resolution | ||||||
![]() | GMP reductase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grenha, R. / Levdikov, V.M. / Blagova, E.V. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S. / Structural Proteomics in Europe (SPINE) | ||||||
![]() | ![]() Title: Crystal Structure of GuaC (BA5705) from Bacillus anthracis at 1.8 A Resolution. Authors: Grenha, R. / Levdikov, V.M. / Blagova, E.V. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.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 | ![]() | 260.9 KB | Display | ![]() |
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PDB format | ![]() | 210.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jr1S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 37183.273 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.2 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: MPD, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2004 / Details: Rh coated Si mirror |
Radiation | Monochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→30 Å / Num. all: 63577 / Num. obs: 63577 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 1.6 / Num. unique all: 6280 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1JR1 Resolution: 1.8→29.85 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.453 / SU ML: 0.102 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.204 / ESU R Free: 0.129 / 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: 25.971 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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