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- PDB-3iwc: T. maritima AdoMetDC complex with S-Adenosylmethionine methyl ester -
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Open data
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Basic information
Entry | Database: PDB / ID: 3iwc | |||||||||
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Title | T. maritima AdoMetDC complex with S-Adenosylmethionine methyl ester | |||||||||
![]() | (S-adenosylmethionine decarboxylase) x 2 | |||||||||
![]() | LYASE / Autocatalytic cleavage / Decarboxylase / Polyamine biosynthesis / Pyruvate / S-adenosyl-L-methionine / Schiff base / Spermidine biosynthesis / Zymogen | |||||||||
Function / homology | ![]() adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / spermidine biosynthetic process / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bale, S. / Kavita, B. / Ealick, S.E. | |||||||||
![]() | ![]() Title: Complexes of Thermotoga maritimaS-adenosylmethionine decarboxylase provide insights into substrate specificity. Authors: Bale, S. / Baba, K. / McCloskey, D.E. / 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 | ![]() | 66.1 KB | Display | ![]() |
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PDB format | ![]() | 47.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 14 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3iwbC ![]() 3iwdC ![]() 1tluS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Details | biological assembly is a dimer in the asymmetric unit |
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Components
#1: Protein | Mass: 6999.928 Da / Num. of mol.: 2 / Fragment: residues 1-62 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9WZC3, adenosylmethionine decarboxylase #2: Protein | Mass: 7807.784 Da / Num. of mol.: 2 / Fragment: residues 64-130 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9WZC3, adenosylmethionine decarboxylase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.18 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2.8 M ammonium formate, 100 mM HEPES, pH 8.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2007 |
Radiation | 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→50 Å / Num. all: 22459 / Num. obs: 22259 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Χ2: 1.317 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2067 / Rsym value: 0.216 / Χ2: 0.544 / % possible all: 90.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1TLU Resolution: 1.9→32.7 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 86489 / 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: 60.519 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.4 Å2 / Biso mean: 32.829 Å2 / Biso min: 14.07 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→32.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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