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Open data
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Basic information
Entry | Database: PDB / ID: 1jen | |||||||||
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Title | HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE | |||||||||
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![]() | S-ADENOSYLMETHIONINE DECARBOXYLASE / PYRUVOYL / GENE DUPLICATION / POLYAMINE BIOSYNTHESIS / SANDWICH / ALLOSTERIC ENZYME | |||||||||
Function / homology | ![]() spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / putrescine binding / spermidine biosynthetic process / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ekstrom, J.L. / Mathews, I.I. / Stanley, B.A. / Pegg, A.E. / Ealick, S.E. | |||||||||
![]() | ![]() 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 | ![]() | 142.4 KB | Display | ![]() |
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PDB format | ![]() | 110.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.9 KB | Display | ![]() |
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Full document | ![]() | 385.4 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.998116, 0.057715, 0.020825), Vector: |
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Components
#1: Protein | Mass: 7694.577 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase #2: Protein | Mass: 30772.105 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 49 % / Description: 22 SELENIUM ATOMS LOCATED IN ASYMMETRIC UNIT | |||||||||||||||
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Crystal grow | pH: 8 / Details: 12 - 16% PEG 8K, 10 MM TRIS-HCL, PH 8.0, pH 8.00 | |||||||||||||||
Crystal | *PLUS Density % sol: 48 % | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: BRANDEIS / Detector: CCD / Date: Sep 1, 1997 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.25→20 Å / Num. obs: 169725 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 15.95 Å2 / Rsym value: 0.05 / Net I/σ(I): 23.71 | ||||||||||||
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 15 / Rsym value: 0.094 / % possible all: 98.1 | ||||||||||||
Reflection | *PLUS Num. obs: 33426 / % possible obs: 98.9 % / Num. measured all: 169725 / Rmerge(I) obs: 0.05 | ||||||||||||
Reflection shell | *PLUS % possible obs: 98.1 % / Rmerge(I) obs: 0.094 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 20.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.35 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.2255 |