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Yorodumi- PDB-2ze3: Crystal Structure of DFA0005 Complexed with alpha-Ketoglutarate: ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ze3 | ||||||
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Title | Crystal Structure of DFA0005 Complexed with alpha-Ketoglutarate: A Novel Member of the ICL/PEPM Superfamily from Alkali-tolerant Deinococcus ficus | ||||||
Components | DFA0005 | ||||||
Keywords | ISOMERASE / Deinococcus ficus / organic waste left-over decomposition / alkaliphilic / ICL/PEPM superfamily / alpha-ketoglutarate ligand | ||||||
Function / homology | Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #510 / Phosphoenolpyruvate-binding domains / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 2-OXOGLUTARIC ACID Function and homology information | ||||||
Biological species | Deinococcus ficus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Liao, C.J. / Chin, K.H. / Chou, S.H. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus Authors: Liao, C.J. / Chin, K.H. / Lin, C.H. / Tsai, P.S. / Lyu, P.C. / Young, C.C. / Wang, A.H. / Chou, S.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ze3.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ze3.ent.gz | 52.2 KB | Display | PDB format |
PDBx/mmJSON format | 2ze3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ze3_validation.pdf.gz | 385.5 KB | Display | wwPDB validaton report |
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Full document | 2ze3_full_validation.pdf.gz | 395 KB | Display | |
Data in XML | 2ze3_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 2ze3_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/2ze3 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/2ze3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29273.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus ficus (bacteria) / Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-AKG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 25, 2007 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 189632 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.059 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.65→18.85 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 223849.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.5821 Å2 / ksol: 0.399115 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→18.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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