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Yorodumi- PDB-2azl: Crystal structure for the mutant F117E of Thermotoga maritima oct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2azl | |||||||||
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Title | Crystal structure for the mutant F117E of Thermotoga maritima octaprenyl pyrophosphate synthase | |||||||||
Components | octoprenyl-diphosphate synthase | |||||||||
Keywords | TRANSFERASE / OPPs / octaprenyl pyrophosphate synthase / Octaprenyl-diphosphate synthase / trans-prenyltransferase / isoprenyl pyrophosphate synthase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.8 Å | |||||||||
Authors | Sun, H.Y. / Ko, T.P. / Kuo, C.J. / Guo, R.T. / Chou, C.C. / Liang, P.H. / Wang, A.H. | |||||||||
Citation | Journal: J.Bacteriol. / Year: 2005 Title: Homodimeric hexaprenyl pyrophosphate synthase from the thermoacidophilic crenarchaeon Sulfolobus solfataricus displays asymmetric subunit structures Authors: Sun, H.Y. / Ko, T.P. / Kuo, C.J. / Guo, R.T. / Chou, C.C. / Liang, P.H. / Wang, A.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2azl.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2azl.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 2azl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2azl_validation.pdf.gz | 427.5 KB | Display | wwPDB validaton report |
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Full document | 2azl_full_validation.pdf.gz | 435.5 KB | Display | |
Data in XML | 2azl_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 2azl_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/2azl ftp://data.pdbj.org/pub/pdb/validation_reports/az/2azl | HTTPS FTP |
-Related structure data
Related structure data | 2azjC 2azkC 1v4eS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33882.277 Da / Num. of mol.: 1 / Mutation: F117E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET-32Xa/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: GenBank: 15644283, UniProt: Q9X1M1*PLUS, EC: 2.5.1.11 |
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#2: 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: 2.74 Å3/Da / Density % sol: 55.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Na+HEPES, Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2005 / Details: mirrors |
Radiation | Monochromator: MIRRORS / 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. obs: 9443 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 76.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 4.2 / Num. unique all: 2166 / Rsym value: 0.526 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1V4E Resolution: 2.8→35.23 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 511274.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.9833 Å2 / ksol: 0.328422 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→35.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
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Xplor file |
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