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- PDB-3ce6: 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: 3ce6 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with NAD and adenosine | ||||||
![]() | 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 | ![]() | 422.8 KB | Display | ![]() |
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PDB format | ![]() | 340.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 92.6 KB | Display | |
Data in CIF | ![]() | 133.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zizC ![]() 2zj0C ![]() 2zj1C ![]() 3dhyC ![]() 1li4S 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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Unit cell |
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Components
#1: Protein | Mass: 54256.219 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-ADN / #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: 2.51 Å3/Da / Density % sol: 51.01 % |
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Crystal grow | Temperature: 291.5 K / pH: 8 Details: 20% PEG 1000, 200 mM Imidazole pH 8.0, 100 mM Calcium acetate, 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: 1.5→100 Å / Num. obs: 308888 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.0487 / Rsym value: 0.0487 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.5→1.54 Å / Rmerge(I) obs: 0.6821 / Mean I/σ(I) obs: 1.48 / Rsym value: 0.6821 / % possible all: 73.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LI4 Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.799 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.099 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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