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- PDB-3ep8: Human AdoMetDC E178Q mutant complexed with S-Adenosylmethionine m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ep8 | |||||||||
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Title | Human AdoMetDC E178Q mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound | |||||||||
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![]() | LYASE / AdoMetDC with mutation in putrescine binding site / Decarboxylase / Pyruvate / S-adenosyl-L-methionine / Spermidine biosynthesis / Zymogen | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Bale, S. / Lopez, M.M. / Makhatadze, G.I. / Fang, Q. / Pegg, A.E. / Ealick, S.E. | |||||||||
![]() | ![]() Title: Structural Basis for Putrescine Activation of Human S-Adenosylmethionine Decarboxylase. Authors: Bale, S. / Lopez, M.M. / Makhatadze, G.I. / Fang, Q. / 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 | ![]() | 82.7 KB | Display | ![]() |
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PDB format | ![]() | 59 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 847.1 KB | Display | ![]() |
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Full document | ![]() | 851.9 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 23 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ep3C ![]() 3ep4C ![]() 3ep5C ![]() 3ep6C ![]() 3ep7C ![]() 3ep9C ![]() 3epaC ![]() 3epbC ![]() 1i7bS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 7694.577 Da / Num. of mol.: 1 / Fragment: UNP residues 1-67 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase |
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#2: Protein | Mass: 29887.230 Da / Num. of mol.: 1 / Fragment: UNP residues 69-328 / Mutation: E178Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase |
#3: Chemical | ChemComp-PYR / |
#4: Chemical | ChemComp-SMM / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 16% PEG 8000, 100 mM Tris, 10 mM DTT, pH 8.0, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. all: 23589 / Num. obs: 23001 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Χ2: 1.079 / Net I/σ(I): 15.005 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2170 / Rsym value: 0.238 / Χ2: 0.683 / % possible all: 91.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1I7B Resolution: 1.97→33.24 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 115700 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.088 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.37 Å2 / Biso mean: 29.257 Å2 / Biso min: 12.76 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.97→33.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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