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Open data
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Basic information
Entry | Database: PDB / ID: 3n1t | ||||||
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Title | Crystal structure of the H101A mutant ecHint GMP complex | ||||||
![]() | HIT-like protein hinT | ||||||
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Function / homology | ![]() D-alanine catabolic process / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cody, V. | ||||||
![]() | ![]() Title: Probing the Impact of the echinT C-Terminal Domain on Structure and Catalysis. Authors: Bardaweel, S. / Pace, J. / Chou, T.F. / Cody, V. / Wagner, C.R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.3 KB | Display | ![]() |
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PDB format | ![]() | 84.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3n1sSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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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Unit cell |
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Components
#1: Protein | Mass: 13191.192 Da / Num. of mol.: 4 / Mutation: H101A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-5GP / ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 40% PEG 20000, 0.1M Magnesium Acetate, 0.1M Sodium Acetate, 20mM Tris pH 7.0, 1 mM EDTA, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 6, 2006 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.716→37.7 Å / Num. all: 41405 / Num. obs: 41372 / % possible obs: 88.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 1.716→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.47 / % possible all: 25.8 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3N1S Resolution: 1.716→35.33 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.382 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.142 / 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: 24.767 Å2
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Refine analyze | Luzzati coordinate error obs: 0.212 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.716→35.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.716→1.76 Å / Total num. of bins used: 20
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