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Yorodumi- PDB-2af7: Crystal structure of the gamma-carboxymuconolactone decarboxylase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2af7 | ||||||
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Title | Crystal structure of the gamma-carboxymuconolactone decarboxylase from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Consortium target TT747. | ||||||
Components | gamma-carboxymuconolactone decarboxylase | ||||||
Keywords | LYASE / Gamma-carboxymuconolactone decarboxylase / O26336_METTH / NESG / TT747 / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | AhpD-like / AhpD-like / Carboxymuconolactone decarboxylase-like / Carboxymuconolactone decarboxylase family / AhpD-like / peroxiredoxin activity / Up-down Bundle / Mainly Alpha / Gamma-carboxymuconolactone decarboxylase Function and homology information | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.81 Å | ||||||
Authors | Vorobiev, S.M. / Kuzin, A. / Skarina, T. / Savchenko, A. / Semesi, A. / Arrowsmith, C. / Edwards, A. / Montelione, G.T. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the gamma-carboxymuconolactone decarboxylase from Methanobacterium thermoautotrophicum. Authors: Vorobiev, S.M. / Kuzin, A. / Skarina, T. / Savchenko, A. / Semesi, A. / Arrowsmith, C. / Edwards, A. / Montelione, G.T. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2af7.cif.gz | 197.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2af7.ent.gz | 170 KB | Display | PDB format |
PDBx/mmJSON format | 2af7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/2af7 ftp://data.pdbj.org/pub/pdb/validation_reports/af/2af7 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14219.488 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: MTH234 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O26336, EC: 4.1.1.44 #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: 3.06 Å3/Da / Density % sol: 54.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10 % PEG 400, 0.1 M potassium chloride, 0.1 M calcium chloride, 0.05 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97628 / Wavelength: 0.97628, 0.9782, 0.9793 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2004 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→30 Å / Num. all: 73566 / Num. obs: 73346 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.118 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.716 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.81→29.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 336208.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.2347 Å2 / ksol: 0.299939 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.81→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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