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Yorodumi- PDB-1v4j: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyper... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v4j | ||||||
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Title | Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima V73Y 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: 2.85 Å | ||||||
Authors | Guo, R.T. / Kuo, C.J. / Chou, C.C. / Ko, T.P. / Shr, H.L. / Liang, P.H. / Wang, A.H.-J. | ||||||
Citation | 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. #1: Journal: To be Published 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v4j.cif.gz | 127.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v4j.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 1v4j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/1v4j ftp://data.pdbj.org/pub/pdb/validation_reports/v4/1v4j | HTTPS FTP |
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-Related structure data
Related structure data | 1v4eSC 1v4hC 1v4iC 1v4kC 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
#1: Protein | Mass: 33964.379 Da / Num. of mol.: 2 / Mutation: V73Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / 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 | ChemComp-SO4 / #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: 2.92 Å3/Da / Density % sol: 57.58 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Na+Hepes, lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. all: 19118 / Num. obs: 18359 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 53.37 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.96 |
Reflection shell | Resolution: 2.85→2.95 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 3.57 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 129154 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V4E Resolution: 2.85→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2
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Displacement parameters | Biso mean: 53.37 Å2 | ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.36 Å / Luzzati sigma a obs: 0.42 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.95 Å / Rfactor Rfree: 0.3026 / Rfactor Rwork: 0.3088 |