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Yorodumi- PDB-1wkz: Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyper... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wkz | ||||||
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Title | Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyperthermophilic Thermotoga Maritima K41A mutant | ||||||
Components | octoprenyl-diphosphate synthase | ||||||
Keywords | TRANSFERASE / trans-type prenyltransferase / thermophilic | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Guo, R.T. / Kuo, C.J. / Cheng, Y.S. / Cheng, Y.L. / Liang, P.H. / Wang, A.H.-J. | ||||||
Citation | Journal: To be Published Title: Biochemical and Structural Basis for Octaprenyl Pyrophosphate Synthase Authors: Guo, R.T. / Kuo, C.J. / Cheng, Y.S. / Cheng, Y.L. / Liang, P.H. / Wang, A.H.-J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Preliminary X-ray diffraction analysis of octaprenyl pyrophosphate synthase crystals from Thermotoga maritima and Escherichia coli Authors: Guo, R.T. / Ko, T.P. / Chou, C.C. / Shr, H.L. / Chu, H.M. / Tsai, Y.H. / Liang, P.H. / Wang, A.H.-J. #2: Journal: J.Biol.Chem. / Year: 2004 Title: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima and Mechanism of Product Chain Length Determination Authors: Guo, R.T. / Kuo, C.J. / Chou, C.C. / Ko, T.P. / Shr, H.L. / Liang, P.H. / Wang, A.H.-J. #3: Journal: Biochemistry / Year: 2004 Title: A Molecular Ruler for Chain Elongation Catalyzed by Octaprenyl Pyrophosphate Synthase and Its Structure-Based Engineering to Produce Unprecedented Long-Chain Trans-Prenyl Products Authors: Guo, R.T. / Kuo, C.J. / Ko, T.P. / 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 | 1wkz.cif.gz | 124.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wkz.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 1wkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1wkz_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 1wkz_full_validation.pdf.gz | 474.7 KB | Display | |
Data in XML | 1wkz_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 1wkz_validation.cif.gz | 36.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/1wkz ftp://data.pdbj.org/pub/pdb/validation_reports/wk/1wkz | HTTPS FTP |
-Related structure data
Related structure data | 1wl0C 1wl1C 1wl2C 1wl3C 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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Unit cell |
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-Components
#1: Protein | Mass: 33842.234 Da / Num. of mol.: 2 / Mutation: K41A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: PET32XA-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1M1, EC: 2.5.1.11 #2: Chemical | #3: 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: 2.86 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Tris-HCl, NaCl, HEPES, Lithium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2004 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. all: 11368 / Num. obs: 10968 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.77 |
Reflection shell | Resolution: 3.4→3.52 Å / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 4.65 / Num. unique all: 1050 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V4E Resolution: 3.4→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 53.49 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.33 Å / Luzzati sigma a obs: 0.37 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.52 Å
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