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Yorodumi- PDB-3tkk: Crystal Structure Analysis of a recombinant predicted acetamidase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tkk | |||||||||
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Title | Crystal Structure Analysis of a recombinant predicted acetamidase/ formamidase from the thermophile thermoanaerobacter tengcongensis | |||||||||
Components | Predicted acetamidase/formamidase | |||||||||
Keywords | HYDROLASE / Beta/Alpha structure | |||||||||
Function / homology | Acetamidase/Formamidase / Acetamidase/Formamidase family / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / metal ion binding / Predicted acetamidase/formamidase Function and homology information | |||||||||
Biological species | Thermoanaerobacter tengcongensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 Å | |||||||||
Authors | Qian, M. / Huang, Q. / Wu, G. / Lai, L. / Tang, Y. / Pei, J. / Kusunoki, M. | |||||||||
Citation | Journal: PROTEIN J. / Year: 2012 Title: Crystal Structure Analysis of a Recombinant Predicted Acetamidase/Formamidase from the Thermophile Thermoanaerobacter tengcongensis. Authors: Qian, M. / Huang, Q. / Wu, G. / Lai, L. / Tang, Y. / Pei, J. / Kusunoki, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tkk.cif.gz | 468.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tkk.ent.gz | 399.1 KB | Display | PDB format |
PDBx/mmJSON format | 3tkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3tkk_validation.pdf.gz | 431.4 KB | Display | wwPDB validaton report |
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Full document | 3tkk_full_validation.pdf.gz | 468 KB | Display | |
Data in XML | 3tkk_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 3tkk_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/3tkk ftp://data.pdbj.org/pub/pdb/validation_reports/tk/3tkk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 32171.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria) Strain: MB4T / Gene: TTE1919 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA DE3 / References: UniProt: Q8R8S5 #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-ZN / #4: 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: 2.42 Å3/Da / Density % sol: 49.21 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M calcium acetate, 0.1M sodium cacodylate, 18%(W/V) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 4, 2004 / Details: mirrors |
Radiation | Monochromator: DOUBLE MIRROR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→99.01 Å / Num. all: 81396 / Num. obs: 75255 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2→2.04 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3778 / % possible all: 64.62 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.99→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.291 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.177 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.712 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2257 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.99→2.041 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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