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- PDB-1msv: The S68A S-adenosylmethionine decarboxylase proenzyme processing ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1msv | ||||||
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Title | The S68A S-adenosylmethionine decarboxylase proenzyme processing mutant. | ||||||
![]() | S-adenosylmethionine decarboxylase proenzyme | ||||||
![]() | LYASE / spermidine biosynthesis / decarboxylase / pyruvate / s-adenosylmethionine / sandwich / allosteric enzyme / pyruvoyl | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tolbert, W.D. / Zhang, Y. / Bennett, E.M. / Cottet, S.E. / Ekstrom, J.L. / Pegg, A.E. / Ealick, S.E. | ||||||
![]() | ![]() Title: Mechanism of Human S-Adenosylmethionine Decarboxylase Proenzyme Processing as Revealed by the Structure of the S68A Mutant. Authors: Tolbert, W.D. / Zhang, Y. / Cottet, S.E. / Bennett, E.M. / Ekstrom, J.L. / Pegg, A.E. / Ealick, S.E. #1: ![]() Title: Structure of a Human S-Adenosylmethionine Decarboxylase Self-Processing Ester Intermediate and Mechanism of Putrescine Stimulation of Processing As Revealed by the H243A Mutant Authors: Ekstrom, J.L. / Tolbert, W.D. / Xiong, H. / Pegg, A.E. / Ealick, S.E. #2: ![]() 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. #3: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.4 KB | Display | ![]() |
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PDB format | ![]() | 120.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1i76S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The proenzyme is a dimer and the dimer is in the asymmetric unit. |
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Components
#1: Protein | Mass: 40625.102 Da / Num. of mol.: 2 / Mutation: S68A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.21 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, tris[hydroxymethyl]aminomethane, dithiothreitol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2001 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→99 Å / Num. all: 82984 / Num. obs: 76221 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.117 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 11752 / Rsym value: 0.28 / % possible all: 96.3 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 99 Å / Num. obs: 82984 / Num. measured all: 551036 / Rmerge(I) obs: 0.117 |
Reflection shell | *PLUS Highest resolution: 1.7 Å / % possible obs: 96.3 % / Num. unique obs: 11752 / Num. measured obs: 41351 / Rmerge(I) obs: 0.28 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1I76 Resolution: 1.75→16.37 Å / Rfactor Rfree error: 0.003 / 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: 34.1972 Å2 / ksol: 0.420892 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.75→16.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.86 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 99 Å / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.76 Å / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.279 |