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Yorodumi- PDB-1t6d: MIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: cryst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t6d | ||||||
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Title | MIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: crystal structure of the type II variant | ||||||
Components | exopolyphosphatase | ||||||
Keywords | HYDROLASE / alpha/beta protein / Actin-like fold | ||||||
Function / homology | Function and homology information guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity / pyrophosphatase activity / nucleobase-containing small molecule interconversion / regulation of transcription by RNA polymerase II / metal ion binding Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Partial model produced by MIRAS phasing / Resolution: 2.15 Å | ||||||
Authors | Kristensen, O. / Laurberg, M. / Liljas, A. / Kastrup, J.S. / Gajhede, M. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family Authors: Kristensen, O. / Laurberg, M. / Liljas, A. / Kastrup, J.S. / Gajhede, M. #1: Journal: Science / Year: 2001 Title: Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli Authors: Kuroda, A. / Nomura, K. / Ohtomo, R. / Kato, J. / Ikeda, T. / Takiguchi, N. / Ohtake, H. / Kornberg, A. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase Authors: Keasling, J.D. / Bertsch, L. / Kornberg, A. #3: Journal: Trends Biochem.Sci. / Year: 1993 Title: Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily Authors: Reizer, J. / Reizer, A. / Saier Jr., M.H. / Bork, P. / Sander, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t6d.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t6d.ent.gz | 111.9 KB | Display | PDB format |
PDBx/mmJSON format | 1t6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t6d_validation.pdf.gz | 460.4 KB | Display | wwPDB validaton report |
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Full document | 1t6d_full_validation.pdf.gz | 473.7 KB | Display | |
Data in XML | 1t6d_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 1t6d_validation.cif.gz | 40.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/1t6d ftp://data.pdbj.org/pub/pdb/validation_reports/t6/1t6d | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological relevant unit is monomeric. |
-Components
#1: Protein | Mass: 36127.094 Da / Num. of mol.: 2 / Mutation: V82M, C138M, V306M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: ppx / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS References: UniProt: O67040, exopolyphosphatase, guanosine-5'-triphosphate,3'-diphosphate phosphatase #2: Chemical | #3: Chemical | ChemComp-TRS / | #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: 2.3 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, PEG400, TRIS, acetic acid, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2001 / Details: Sagitally focusing Ge(220) and a multilayer |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. all: 66436 / Num. obs: 66436 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 8.8 / Num. unique all: 10090 / Rsym value: 0.287 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Partial model produced by MIRAS phasing Resolution: 2.15→29.06 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2055074.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Anomalous data was used in refinement.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.2396 Å2 / ksol: 0.335738 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→29.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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