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Yorodumi- PDB-1iy1: Crystal structure of the FtsH ATPase domain with ADP from Thermus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iy1 | ||||||
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Title | Crystal structure of the FtsH ATPase domain with ADP from Thermus thermophilus | ||||||
Components | ATP-dependent metalloprotease FtsH | ||||||
Keywords | HYDROLASE / AAA domain fold | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / ATP-dependent peptidase activity / protein catabolic process / metalloendopeptidase activity / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Niwa, H. / Tsuchiya, D. / Makyio, H. / Yoshida, M. / Morikawa, K. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8 Authors: Niwa, H. / Tsuchiya, D. / Makyio, H. / Yoshida, M. / Morikawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iy1.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iy1.ent.gz | 40.3 KB | Display | PDB format |
PDBx/mmJSON format | 1iy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/1iy1 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/1iy1 | HTTPS FTP |
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-Related 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: 27385.463 Da / Num. of mol.: 1 / Fragment: F1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: FtsH / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9LCZ4, UniProt: Q5SI82*PLUS |
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#2: Chemical | ChemComp-ADP / |
#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: 2.43 Å3/Da / Density % sol: 49.43 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Ammonium sulfate, Tris-HCl, ADP, magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 6, 2001 |
Radiation | Monochromator: OSMIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 6477 / Num. obs: 6399 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 99.1 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS Lowest resolution: 3 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→12 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→12 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 12 Å / Num. reflection obs: 5835 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.207 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.338 / Rfactor Rwork: 0.259 |