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- PDB-4qez: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocystein... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qez | ||||||
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Title | Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Bacillus anthracis | ||||||
![]() | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | ||||||
![]() | HYDROLASE / Amino-acid biosynthesis / Methionine biosynthesis | ||||||
Function / homology | ![]() nucleoside catabolic process / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tarique, K.F. / Devi, S. / Abdul Rehman, S.A. / Gourinath, S. | ||||||
![]() | ![]() Title: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Bacillus anthracis Authors: Tarique, K.F. / Devi, S. / Abdul Rehman, S.A. / Gourinath, 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 | ![]() | 272.4 KB | Display | ![]() |
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PDB format | ![]() | 224 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 478.2 KB | Display | ![]() |
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Full document | ![]() | 489 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dp9S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 26353.990 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q81LL4, adenosylhomocysteine nucleosidase #2: Chemical | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2M Ammonium sulfate, 0.2M MgCl2, Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 16291 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.08 / Net I/σ(I): 21.64 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.549 / Rsym value: 0.34 / % possible all: 75 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DP9 Resolution: 2.7→34.49 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.895 / SU B: 40.202 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / 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 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.475 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→34.49 Å
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Refine LS restraints |
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