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- PDB-2zj0: Crystal structure of Mycobacterium tuberculosis S-Adenosyl-L-homo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zj0 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis S-Adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 2-fluoroadenosine | ||||||
![]() | Adenosylhomocysteinase | ||||||
![]() | HYDROLASE / Protein-substrate complex / dimer of dimers / NAD binding domain / 37 amino acid insertional region / One-carbon metabolism | ||||||
Function / homology | ![]() adenosylhomocysteinase / methionine catabolic process / adhesion of symbiont to host cell / adenosine metabolic process / adenosylhomocysteinase / adenosylhomocysteinase activity / entry of bacterium into host cell / S-adenosylmethionine cycle / zymogen binding / NAD+ binding ...adenosylhomocysteinase / methionine catabolic process / adhesion of symbiont to host cell / adenosine metabolic process / adenosylhomocysteinase / adenosylhomocysteinase activity / entry of bacterium into host cell / S-adenosylmethionine cycle / zymogen binding / NAD+ binding / peptidoglycan-based cell wall / one-carbon metabolic process / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reddy, M.C.M. / Gokulan, K. / Shetty, N.D. / Owen, J.L. / Ioerger, T.R. / Sacchettini, J.C. | ||||||
![]() | ![]() Title: Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors. Authors: Reddy, M.C. / Kuppan, G. / Shetty, N.D. / Owen, J.L. / Ioerger, T.R. / Sacchettini, J.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 | ![]() | 392.2 KB | Display | ![]() |
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PDB format | ![]() | 320.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 80.9 KB | Display | |
Data in CIF | ![]() | 110.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zizC ![]() 2zj1C ![]() 3ce6SC ![]() 3dhyC C: citing same article ( 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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Unit cell |
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Components
#1: Protein | Mass: 54387.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P60176, UniProt: P9WGV3*PLUS, adenosylhomocysteinase #2: Chemical | ChemComp-2FA / #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.53 % |
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Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Magnesium chloride, 0.1 M Tris-HCl pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2005 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→100 Å / Num. all: 74187 / Num. obs: 70373 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 35.92 Å2 / Rmerge(I) obs: 0.0809 / Rsym value: 0.0809 / Net I/σ(I): 10.52 |
Reflection shell | Resolution: 2.42→2.49 Å / Rmerge(I) obs: 0.406 / Rsym value: 0.406 / % possible all: 79.54 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3CE6 Resolution: 2.42→33.15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.889 / SU B: 10.628 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.769 / ESU R Free: 0.338 / 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: 38.276 Å2
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Refinement step | Cycle: LAST / Resolution: 2.42→33.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.42→2.49 Å / Total num. of bins used: 20
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