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Yorodumi- PDB-1iy2: Crystal structure of the FtsH ATPase domain from Thermus thermophilus -
+Open data
-Basic information
Entry | Database: PDB / ID: 1iy2 | ||||||
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Title | Crystal structure of the FtsH ATPase domain 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: 3.2 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 | 1iy2.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iy2.ent.gz | 39.6 KB | Display | PDB format |
PDBx/mmJSON format | 1iy2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1iy2_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 1iy2_full_validation.pdf.gz | 447.8 KB | Display | |
Data in XML | 1iy2_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 1iy2_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/1iy2 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/1iy2 | HTTPS FTP |
-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: 29938.297 Da / Num. of mol.: 1 / Fragment: F2 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-SO4 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
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Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 4, 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: 3.2→50 Å / Num. all: 5112 / Num. obs: 4964 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.2→3.4 Å / % possible all: 92.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.125 |
Reflection shell | *PLUS % possible obs: 92.6 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 5.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rfree: 0.294 / Rfactor Rwork: 0.253 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 0.9 | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 3.2 Å / Rfactor Rfree: 0.419 / Rfactor Rwork: 0.335 |