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Yorodumi- PDB-2zd0: Crystal structures and thermostability of mutant TRAP3 A5 (ENGINE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zd0 | ||||||
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Title | Crystal structures and thermostability of mutant TRAP3 A5 (ENGINEERED TRAP) | ||||||
Components | Transcription attenuation protein mtrB | ||||||
Keywords | RNA BINDING PROTEIN / LINKER / ARTIFICIAL / ENGINEERED / RING PROTEIN / 12-mer | ||||||
Function / homology | Function and homology information DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Watanabe, M. / Mishima, Y. / Yamashita, I. / Park, S.Y. / Tame, J.R.H. / Heddle, J.G. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Intersubunit linker length as a modifier of protein stability: crystal structures and thermostability of mutant TRAP. Authors: Watanabe, M. / Mishima, Y. / Yamashita, I. / Park, S.Y. / Tame, J.R. / Heddle, J.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zd0.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zd0.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zd/2zd0 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/2zd0 | HTTPS FTP |
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-Related structure data
Related structure data | 2zczC 2exsS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | THE POLYPEPTIDE CHAIN CONTAINS THREE (3) COPIES OF THE TRAP PROTEIN LINKED IN TANDEM, WHICH ARRANGE THEMSELVES TO MAKE A 12-MER RING IN SOLUTION. EACH CHAIN IN THIS MODEL REPRESENTS ONE COPY OF TRAP, NOT A SEPARATE POLYPEPTIDE. THE LINKER PEPTIDES ARE NOT VISIBLE IN THE ELECTRON DENSITY. THE 12MER RINGS ARE ALIGNED WITH THE CRYSTALLOGRAPHIC FOUR-FOLD AXIS. THERE ARE THREE COPIES OF TRAP PRESENT IN THE ASYMMETRIC UNIT. FOR THIS PROTEIN, CALLED T3A5, THE LINKER PEPTIDES CONSIST OF FIVE (5) ALANINE RESIDUES. |
-Components
#1: Protein | Mass: 8612.765 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: NCA 26, ATCC 12980 / Gene: mtrB / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X6J6 #2: Chemical | #3: 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: 2.14 Å3/Da / Density % sol: 42.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 0.09M CAPS pH 10.5, 30%(w/v) PEG300, 0.15M Ammonium sulfate, 10mM L-tryptophan, 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: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 7, 2006 / Details: mirrors |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 7898 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.048 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 11.7 / Num. unique all: 744 / Rsym value: 0.246 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2EXS Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.967 / SU ML: 0.185 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.609 / ESU R Free: 0.301 / 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: 27.491 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.497→2.561 Å / Rfactor Rfree error: 0.08 / Total num. of bins used: 20
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