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Yorodumi- PDB-3h0w: Human AdoMetDC with 5'-Deoxy-5'-[(N-dimethyl)amino]-8-methyl-adenosine -
+Open data
-Basic information
Entry | Database: PDB / ID: 3h0w | |||||||||
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Title | Human AdoMetDC with 5'-Deoxy-5'-[(N-dimethyl)amino]-8-methyl-adenosine | |||||||||
Components | (S-adenosylmethionine decarboxylase ...Adenosylmethionine decarboxylase) x 2 | |||||||||
Keywords | LYASE / AdoMetDC with competitive substrate analogs / Autocatalytic cleavage / Decarboxylase / Phosphoprotein / Polyamine biosynthesis / Pyruvate / S-adenosyl-L-methionine / Schiff base / 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: 1.81 Å | |||||||||
Authors | Bale, S. / Brooks, W.H. / Hanes, J.W. / Mahesan, A.M. / Guida, W.C. / Ealick, S.E. | |||||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Role of the sulfonium center in determining the ligand specificity of human s-adenosylmethionine decarboxylase. Authors: Bale, S. / Brooks, W. / Hanes, J.W. / Mahesan, A.M. / Guida, W.C. / 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 | 3h0w.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h0w.ent.gz | 59.5 KB | Display | PDB format |
PDBx/mmJSON format | 3h0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/3h0w ftp://data.pdbj.org/pub/pdb/validation_reports/h0/3h0w | HTTPS FTP |
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-Related structure data
Related structure data | 3h0vC 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 on special symmetry positions |
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-Components
-S-adenosylmethionine decarboxylase ... , 2 types, 2 molecules BA
#1: Protein | Mass: 7694.577 Da / Num. of mol.: 1 / Fragment: residues 1-67 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P17707, adenosylmethionine decarboxylase |
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#2: Protein | Mass: 30615.945 Da / Num. of mol.: 1 / Fragment: residues 69-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AMD1, AMD / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P17707, adenosylmethionine decarboxylase |
-Non-polymers , 4 types, 223 molecules
#3: Chemical | ChemComp-PUT / |
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#4: Chemical | ChemComp-N8M / |
#5: Chemical | ChemComp-PYR / |
#6: 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: 2.19 Å3/Da / Density % sol: 43.93 % |
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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: Jun 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: 1.81→50 Å / Num. all: 29093 / Num. obs: 28205 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Χ2: 1.173 / Net I/σ(I): 17.715 |
Reflection shell | Resolution: 1.81→1.87 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2219 / Rsym value: 0.215 / Χ2: 0.66 / % possible all: 73.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1I7B Resolution: 1.81→47.96 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 127036 / 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: 31.108 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.14 Å2 / Biso mean: 28.152 Å2 / Biso min: 10.68 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.81→47.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.92 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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