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Yorodumi- PDB-1tmi: Structure of Thermotoga maritima S63A non-processing mutant S-ade... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tmi | ||||||
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Title | Structure of Thermotoga maritima S63A non-processing mutant S-adenosylmethionine decarboxylase | ||||||
Components | S-adenosylmethionine decarboxylase proenzyme, AdoMetDC, SamDC | ||||||
Keywords | LYASE / two-layer alpha beta-sandwich | ||||||
Function / homology | Function and homology information adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / spermidine biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Toms, A.V. / Kinsland, C. / McCloskey, D.E. / Pegg, A.E. / Ealick, S.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Evolutionary Links as Revealed by the Structure of Thermotoga maritima S-Adenosylmethionine Decarboxylase. Authors: Toms, A.V. / Kinsland, C. / McCloskey, D.E. / 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 | 1tmi.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tmi.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 1tmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/1tmi ftp://data.pdbj.org/pub/pdb/validation_reports/tm/1tmi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer. The asymmetric unit contains 1 biological unit. |
-Components
#1: Protein | Mass: 14790.736 Da / Num. of mol.: 2 / Mutation: S63A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: SPEH, TM0655 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)pRare References: UniProt: Q9WZC3, adenosylmethionine decarboxylase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 295.4 K / Method: vapor diffusion, hanging drop / pH: 8 Details: ammonium formate, HEPES, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 295.4K |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9792,0.9793,0.9641 | ||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→32.5 Å / Num. all: 31186 / Num. obs: 30984 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.048 / Net I/σ(I): 30.7 | ||||||||||||
Reflection shell | Resolution: 1.7→1.81 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.385 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→32.47 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 410997.27 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: twinning operator was used to ensure that pairs of twin related reflections were in the same set
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.8139 Å2 / ksol: 0.391508 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→32.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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