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Open data
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Basic information
Entry | Database: PDB / ID: 3epb | |||||||||
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Title | Human AdoMetDC E256Q mutant complexed with putrescine | |||||||||
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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 / putrescine binding / polyamine metabolic process / 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 | ![]() | 81.9 KB | Display | ![]() |
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PDB format | ![]() | 59.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ep3C ![]() 3ep4C ![]() 3ep5C ![]() 3ep6C ![]() 3ep7C ![]() 3ep8C ![]() 3ep9C ![]() 3epaC ![]() 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
#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: 29887.234 Da / Num. of mol.: 1 / Fragment: UNP residues 69-328 / Mutation: E256Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase |
#3: Chemical | ChemComp-PUT / |
#4: Chemical | ChemComp-PYR / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.03 % |
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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: Mar 1, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 34072 / Num. obs: 33438 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Χ2: 0.953 / Net I/σ(I): 30.146 |
Reflection shell | Resolution: 1.75→1.81 Å / Redundancy: 3 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3110 / Rsym value: 0.158 / Χ2: 0.517 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1I7B Resolution: 1.75→35.3 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 205376 / 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: 38.048 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.77 Å2 / Biso mean: 31.517 Å2 / Biso min: 12.88 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→35.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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