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- PDB-1i79: HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1i79 | |||||||||
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Title | HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COVALENTLY BOUND 5'-DEOXY-5'-[(3-HYDRAZINOPROPYL)METHYLAMINO]ADENOSINE | |||||||||
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![]() | LYASE / Spermidine biosynthesis / Decarboxylase / Pyruvate / S-ADENOSYLMETHIONINE / SANDWICH / ALLOSTERIC ENZYME / PYRUVOYL | |||||||||
Function / homology | ![]() spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / putrescine binding / spermidine biosynthetic process / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tolbert, W.D. / Ekstrom, J.L. / Mathews, I.I. / Secrist III, J.A. / Pegg, A.E. / Ealick, S.E. | |||||||||
![]() | ![]() Title: The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase. Authors: Tolbert, W.D. / Ekstrom, J.L. / Mathews, I.I. / Secrist III, J.A. / Kapoor, P. / Pegg, A.E. / Ealick, S.E. #1: ![]() Title: The Crystal Structure of Human S-adenosylmethionine Decarboxylase at 2.25 A Resolution Reveals a Novel Fold Authors: Ekstrom, J.L. / Mathews, I.I. / Stanley, B.A. / Pegg, A.E. / Ealick, S.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84 KB | Display | ![]() |
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PDB format | ![]() | 60.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 774.7 KB | Display | ![]() |
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Full document | ![]() | 778.8 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | The native enzyme is a dimer generated by the crystallographic two-fold. |
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Components
#1: Protein | Mass: 7694.577 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase |
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#2: Protein | Mass: 30671.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase |
#3: Chemical | ChemComp-MHZ / |
#4: Chemical | ChemComp-PUT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.98 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, Tris-HCl pH 8.0, dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2000 |
Radiation | Monochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→100 Å / Num. all: 22266 / Num. obs: 21309 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.01→2.15 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.4 / % possible all: 95.3 |
Reflection | *PLUS Num. measured all: 78987 |
Reflection shell | *PLUS % possible obs: 95.3 % / Rmerge(I) obs: 0.25 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 25.12 Å2 / ksol: 0.358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→25.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.01→2.14 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.8 % / Rfactor obs: 0.212 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.326 / % reflection Rfree: 10 % / Rfactor Rwork: 0.278 |