+Open data
-Basic information
Entry | Database: PDB / ID: 2hut | ||||||
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Title | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | ||||||
Components | Probable 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 / DIFFERENCE FOURIER / Resolution: 2.4 Å | ||||||
Authors | Sugahara, M. / Saraboji, K. / Malathy sony, S.M. / Ponnuswamy, M.N. / Kumarevel, T.S. / 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. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hut.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hut.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/2hut ftp://data.pdbj.org/pub/pdb/validation_reports/hu/2hut | HTTPS FTP |
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-Related structure data
Related structure data | 2e8hC 2hr8C 2huqC 2huvC 2huxC 2owfC 2owgC 2owkC 2owuC 2owvC 2p2xC 2p5cC 2p5fC 2p6dC 2p6iC 2p6kC 2p6lC 2p9dC 2pb4C 2pb5C 2pb6C 2pcaC 2pcgC 2pchC 2pciC 2pckC 2pcmC 1vceS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | The biological assembly is a dimer in the asymmetric unit |
-Components
#1: Protein | Mass: 29631.404 Da / Num. of mol.: 2 / Mutation: L72M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58456, diphthine synthase #2: Chemical | ChemComp-SAH / | #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: 3.25 Å3/Da / Density % sol: 62.13 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 7 Details: Sodium malonate, MES, pH 7.0, 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 VII / Detector: IMAGE PLATE / Date: Nov 30, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. all: 31141 / Num. obs: 31141 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 53.76 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.059 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 4.3 / Num. unique all: 3036 / Rsym value: 0.555 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1VCE Resolution: 2.4→14.99 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: 46.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→14.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.028
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