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Yorodumi- PDB-2azj: Crystal structure for the mutant D81C of Sulfolobus solfataricus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2azj | |||||||||
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Title | Crystal structure for the mutant D81C of Sulfolobus solfataricus hexaprenyl pyrophosphate synthase | |||||||||
Components | Geranylgeranyl pyrophosphate synthetase | |||||||||
Keywords | TRANSFERASE / HexPPs / trans-prenyltransferase | |||||||||
Function / homology | Function and homology information hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific] / hexaprenyl diphosphate synthase (geranylgeranyl-diphosphate specific) activity / plastoquinone biosynthetic process / transferase complex / prenyltransferase activity / ubiquinone biosynthetic process / isoprenoid biosynthetic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Sulfolobus solfataricus (archaea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å | |||||||||
Authors | Sun, H.Y. / Ko, T.P. / Kuo, C.J. / Guo, R.T. / Chou, C.C. / Liang, P.H. / Wang, A.H.J. | |||||||||
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.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2azj.cif.gz | 128.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2azj.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 2azj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2azj_validation.pdf.gz | 440.2 KB | Display | wwPDB validaton report |
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Full document | 2azj_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 2azj_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 2azj_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/2azj ftp://data.pdbj.org/pub/pdb/validation_reports/az/2azj | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 33332.016 Da / Num. of mol.: 2 / Mutation: D81C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: gdS-2 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: GenBank: 15899101, UniProt: Q97W92*PLUS, dimethylallyltranstransferase #2: 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: 2.35 Å3/Da / Density % sol: 47.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 6000, lithium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 21, 2004 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 23556 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 33.1 Å2 / Rsym value: 0.049 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 3.7 / Num. unique all: 2341 / Rsym value: 0.52 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.4→48.37 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 26602820.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.3581 Å2 / ksol: 0.305145 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→48.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Xplor file |
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