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Yorodumi- PDB-3ep6: Human AdoMetDC D174N mutant complexed with S-Adenosylmethionine m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ep6 | |||||||||
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Title | Human AdoMetDC D174N mutant complexed with S-Adenosylmethionine methyl ester and no putrescine bound | |||||||||
Components |
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Keywords | LYASE / AdoMetDC with mutation in putrescine binding site / Decarboxylase / Pyruvate / S-adenosyl-L-methionine / Spermidine biosynthesis / Zymogen | |||||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Bale, S. / Lopez, M.M. / Makhatadze, G.I. / Fang, Q. / Pegg, A.E. / Ealick, S.E. | |||||||||
Citation | Journal: Biochemistry / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ep6.cif.gz | 81.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ep6.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ep6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ep6_validation.pdf.gz | 841.1 KB | Display | wwPDB validaton report |
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Full document | 3ep6_full_validation.pdf.gz | 845.5 KB | Display | |
Data in XML | 3ep6_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 3ep6_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/3ep6 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/3ep6 | HTTPS FTP |
-Related structure data
Related structure data | 3ep3C 3ep4C 3ep5C 3ep7C 3ep8C 3ep9C 3epaC 3epbC 1i7bS S: Starting model for refinement C: citing same article (ref.) |
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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: 7694.577 Da / Num. of mol.: 1 / Fragment: UNP residues 1-67 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE-C145S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: D174N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE-C145S / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P17707, adenosylmethionine decarboxylase |
#3: Chemical | ChemComp-PYR / |
#4: Chemical | ChemComp-SMM / |
#5: 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: 2.22 Å3/Da / Density % sol: 44.61 % |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 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: 1.7→50 Å / Num. all: 35113 / Num. obs: 33418 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Χ2: 1.386 / Net I/σ(I): 15.374 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2801 / Rsym value: 0.328 / Χ2: 0.944 / % possible all: 78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I7B Resolution: 1.7→47.93 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 648036 / 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: 44.249 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.48 Å2 / Biso mean: 30.914 Å2 / Biso min: 15.39 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→47.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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