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Yorodumi- PDB-2nzc: The structure of uncharacterized protein TM1266 from Thermotoga m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nzc | ||||||
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Title | The structure of uncharacterized protein TM1266 from Thermotoga maritima. | ||||||
Components | Hypothetical protein | ||||||
Keywords | Structural Genomics/Unknown Function / Thermotoga maritima / sturctural genomics / TM1266 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Structural Genomics-Unknown Function COMPLEX | ||||||
Function / homology | Function and homology information [FeFe]-hydrogenase system regulator TM1266 / Iron-only hydrogenase system regulator, putative / ACT-like. Chain A, domain 2 / Acetolactate synthase/Transcription factor NikR, C-terminal / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Cuff, M.E. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: The structure of uncharacterized protein TM1266 from Thermotoga maritima. Authors: Cuff, M.E. / Evdokimova, E. / Kudritska, M. / Edwards, A. / Joachimiak, A. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nzc.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nzc.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 2nzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nzc_validation.pdf.gz | 454.2 KB | Display | wwPDB validaton report |
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Full document | 2nzc_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 2nzc_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 2nzc_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/2nzc ftp://data.pdbj.org/pub/pdb/validation_reports/nz/2nzc | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-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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Details | The biological assembly is likely to be a tetramer, the contents of the asymmetric unit. It has not been experimentally verified. |
-Components
#1: Protein | Mass: 9909.197 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9X0Z3 #2: Chemical | ChemComp-PO4 / | #3: Chemical | ChemComp-ACY / #4: Chemical | ChemComp-GOL / | #5: 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: 1.96 Å3/Da / Density % sol: 37.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1 M ammonium dihydrogen phosphate, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97924, 0.97938 | |||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Apr 10, 2005 | |||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.95→33.4 Å / Num. all: 22828 / Num. obs: 22928 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 37.3 Å2 / Net I/σ(I): 7 | |||||||||
Reflection shell | Resolution: 1.95→2.001 Å / Redundancy: 4.6 % / % possible all: 98.51 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→33.43 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.282 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.223 / ESU R Free: 0.189 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 37.317 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→33.43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 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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