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Yorodumi- PDB-1i7b: HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i7b | |||||||||
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Title | HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE WITH COVALENTLY BOUND PYRUVOYL GROUP AND COVALENTLY BOUND S-ADENOSYLMETHIONINE METHYL ESTER | |||||||||
Components |
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Keywords | LYASE / Spermidine biosynthesis / Decarboxylase / Pyruvate / S-ADENOSYLMETHIONINE / SANDWICH / ALLOSTERIC ENZYME / PYRUVOYL | |||||||||
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: 1.9 Å | |||||||||
Authors | Tolbert, W.D. / Ekstrom, J.L. / Mathews, I.I. / Secrist III, J.A. / Pegg, A.E. / Ealick, S.E. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase. Authors: Tolbert, W.D. / Ekstrom, J.L. / Mathews, I.I. / Secrist III, J.A. / Kapoor, P. / Pegg, A.E. / Ealick, S.E. #1: Journal: Structure / Year: 1999 Title: The Crystal Structure of Human S-adenosylmethionine Decarboxylase at 2.25 A Resolution Reveals a Novel Fold Authors: Ekstrom, J.L. / Mathews, I.I. / Stanley, B.A. / 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 | 1i7b.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i7b.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 1i7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i7b_validation.pdf.gz | 811.7 KB | Display | wwPDB validaton report |
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Full document | 1i7b_full_validation.pdf.gz | 815.8 KB | Display | |
Data in XML | 1i7b_validation.xml.gz | 16 KB | Display | |
Data in CIF | 1i7b_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/1i7b ftp://data.pdbj.org/pub/pdb/validation_reports/i7/1i7b | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The native enzyme is a dimer generated by the crystallographic two-fold. |
-Components
#1: Protein | Mass: 7694.577 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P17707, adenosylmethionine decarboxylase |
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#2: Protein | Mass: 30671.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P17707, adenosylmethionine decarboxylase |
#3: Chemical | ChemComp-SMM / |
#4: Chemical | ChemComp-PUT / |
#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: 2.2 Å3/Da / Density % sol: 44.22 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, Tris-HCl pH 8.0, dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 291K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 26, 2000 |
Radiation | Monochromator: Si 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. all: 26667 / Num. obs: 26560 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.2 / % possible all: 99.8 |
Reflection | *PLUS Num. measured all: 94520 |
Reflection shell | *PLUS % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.22 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 285249.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.05 Å2 / ksol: 0.401 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→27.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.279 / Rfactor Rwork: 0.238 |