+Open data
-Basic information
Entry | Database: PDB / ID: 2owf | ||||||
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Title | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | ||||||
Components | diphthine synthase | ||||||
Keywords | TRANSFERASE / Pyrococcus horikoshii OT3 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information diphthine synthase / diphthine synthase activity / protein histidyl modification to diphthamide / methylation Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sugahara, M. / Morikawa, Y. / Matsuura, Y. / Shimada, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of PH0725 from Pyrococcus horikoshii OT3 Authors: Sugahara, M. / Morikawa, Y. / Matsuura, Y. / Shimada, H. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2owf.cif.gz | 71.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2owf.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 2owf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/2owf ftp://data.pdbj.org/pub/pdb/validation_reports/ow/2owf | HTTPS FTP |
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-Related structure data
Related structure data | 2e8hC 2hr8C 2huqC 2hutC 2huvC 2huxC 2owgC 2owkC 2owuC 2owvC 2p2xC 2p5cC 2p5fC 2p6dC 2p6iC 2p6kC 2p6lC 2p9dC 2pb4C 2pb5C 2pb6C 2pcaC 2pcgC 2pchC 2pciC 2pckC 2pcmC 1wngS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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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Details | The biological assembly is a dimer. |
-Components
#1: Protein | Mass: 29558.354 Da / Num. of mol.: 1 / Mutation: W143M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: O58456, diphthine synthase |
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#2: Chemical | ChemComp-SAH / |
#3: 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: 3.64 Å3/Da / Density % sol: 66.19 % |
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Crystal grow | Temperature: 295 K / Method: oil microbatch / pH: 5.5 Details: 3.86M Sodium formate, 0.1M Acetate, pH 5.5, oil microbatch, temperature 295K |
-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 / Date: Sep 11, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 22826 / Num. obs: 22826 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.5 % / Biso Wilson estimate: 35.67 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.087 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 18.6 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2208 / Rsym value: 0.578 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1wng Resolution: 2.2→19.79 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.026
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