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- PDB-1mhm: Crystal structure of S-adenosylmethionine decarboxylase from potato -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mhm | |||||||||
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Title | Crystal structure of S-adenosylmethionine decarboxylase from potato | |||||||||
![]() | (S-adenosylmethionine decarboxylase) x 2 | |||||||||
![]() | LYASE / covalent pyruvoyl group | |||||||||
Function / homology | ![]() : / spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / spermidine biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Bennett, E.M. / Ekstrom, J.L. / Pegg, A.E. / Ealick, S.E. | |||||||||
![]() | ![]() Title: Monomeric S-Adenosylmethionine Decarboxylase from Plants Provides an Alternative to Putrescine Stimulation Authors: Bennett, E.M. / Ekstrom, J.L. / 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 | ![]() | 75 KB | Display | ![]() |
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PDB format | ![]() | 54.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 371.7 KB | Display | ![]() |
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Full document | ![]() | 378 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 7886.826 Da / Num. of mol.: 1 / Fragment: beta chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q04694, adenosylmethionine decarboxylase |
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#2: Protein | Mass: 31882.322 Da / Num. of mol.: 1 / Fragment: alpha chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q04694, adenosylmethionine decarboxylase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.48 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: trisodium citrate, isopropanol, PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→99 Å / Num. all: 20754 / Num. obs: 18907 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.1→2.18 Å / Rsym value: 0.409 / % possible all: 79.1 |
Reflection | *PLUS Num. obs: 17049 / % possible obs: 90.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS Highest resolution: 2.26 Å / Lowest resolution: 2.37 Å / % possible obs: 69.6 % / Redundancy: 2.8 % / Num. unique obs: 1084 / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine analyze | Luzzati coordinate error free: 0.4 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å
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Xplor file |
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Refinement | *PLUS Lowest resolution: 500 Å | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.398 / Num. reflection Rfree: 61 / Num. reflection obs: 1070 |