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Yorodumi- PDB-3dhy: Crystal Structures of Mycobacterium tuberculosis S-Adenosyl-L-Hom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dhy | ||||||
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Title | Crystal Structures of Mycobacterium tuberculosis S-Adenosyl-L-Homocysteine Hydrolase in Ternary Complex with Substrate and Inhibitors | ||||||
Components | Adenosylhomocysteinase | ||||||
Keywords | HYDROLASE / Protein-substrate complex / dimer of dimers / NAD binding domain / 37 amino acid insertion / solvent access channel / Structural Genomics / Tuberculosis structural genomics Consortium / TB Structural Genomics Consortium / TBSGC / Cytoplasm / NAD / One-carbon metabolism / PSI-2 / Protein Structure Initiative | ||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shetty, N.D. / Ioerger, T.R. / Gokulan, K. / Reddy, M.C.M. / Owen, J.L. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Protein Sci. / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dhy.cif.gz | 385.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dhy.ent.gz | 315.6 KB | Display | PDB format |
PDBx/mmJSON format | 3dhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dhy_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 3dhy_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 3dhy_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 3dhy_validation.cif.gz | 63.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/3dhy ftp://data.pdbj.org/pub/pdb/validation_reports/dh/3dhy | HTTPS FTP |
-Related structure data
Related structure data | 2zizC 2zj0C 2zj1C 3ce6SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: ahcY, sahH, Rv3248c, MT3346, MTCY20B11.23c / Plasmid: pET28TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P60176, UniProt: P9WGV3*PLUS, adenosylhomocysteinase #2: Chemical | ChemComp-3DH / #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.92 % |
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Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M MgCl2, 0.1 M Tris 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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2008 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→99.5 Å / Num. obs: 384395 / % possible obs: 58.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.309 / Net I/σ(I): 2 |
Reflection shell | Resolution: 1.19→1.23 Å / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 0.7 / % possible all: 3.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3CE6 Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.529 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.279 / 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: 35.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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