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Yorodumi- PDB-1mhm: Crystal structure of S-adenosylmethionine decarboxylase from potato -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mhm | |||||||||
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Title | Crystal structure of S-adenosylmethionine decarboxylase from potato | |||||||||
Components | (S-adenosylmethionine decarboxylaseAdenosylmethionine decarboxylase) x 2 | |||||||||
Keywords | LYASE / covalent pyruvoyl group | |||||||||
Function / homology | Function and homology information : / spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / spermidine biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | Solanum tuberosum (potato) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Bennett, E.M. / Ekstrom, J.L. / Pegg, A.E. / Ealick, S.E. | |||||||||
Citation | Journal: Biochemistry / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mhm.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mhm.ent.gz | 54.2 KB | Display | PDB format |
PDBx/mmJSON format | 1mhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/1mhm ftp://data.pdbj.org/pub/pdb/validation_reports/mh/1mhm | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Solanum tuberosum (potato) / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 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.) Solanum tuberosum (potato) / Plasmid: pQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: Q04694, adenosylmethionine decarboxylase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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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 |