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Yorodumi- PDB-2zk7: Structure of a C-terminal deletion mutant of Thermoplasma acidoph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zk7 | ||||||
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Title | Structure of a C-terminal deletion mutant of Thermoplasma acidophilum aldohexose dehydrogenase (AldT) | ||||||
Components | Glucose 1-dehydrogenase related protein | ||||||
Keywords | OXIDOREDUCTASE / ROSSMANN FOLD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Nishioka, T. / Yasutake, Y. / Nishiya, Y. / Tamura, N. / Tamura, T. | ||||||
Citation | Journal: Proteins / Year: 2009 Title: C-terminal tail derived from the neighboring subunit is critical for the activity of Thermoplasma acidophilum D-aldohexose dehydrogenase Authors: Nishioka, T. / Yasutake, Y. / Nishiya, Y. / Tamura, N. / Tamura, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zk7.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zk7.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/2zk7 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/2zk7 | HTTPS FTP |
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-Related structure data
Related structure data | 2dtdS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28298.395 Da / Num. of mol.: 2 Mutation: C-terminal deletion (residues 250-255 are deleted) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0754 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9HK51, EC: 1.1.1.118 #2: Water | ChemComp-HOH / | Sequence details | SIX C-TERMINAL RESIDUES(250-255) ARE DELETED. | |
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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 Å3/Da / Density % sol: 38.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M imidazol, 0.8M Na/K tartrate, 0.1M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 21, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 13725 / Num. obs: 13725 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 18.5 % / Biso Wilson estimate: 74.2 Å2 / Rsym value: 0.106 / Net I/σ(I): 43.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 18.4 % / Mean I/σ(I) obs: 7.9 / Num. unique all: 1308 / Rsym value: 0.611 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DTD Resolution: 2.71→40.72 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / SU B: 37.95 / SU ML: 0.363 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.567 Å2
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Refinement step | Cycle: LAST / Resolution: 2.71→40.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.707→2.777 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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