+Open data
-Basic information
Entry | Database: PDB / ID: 2p6l | ||||||
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Title | Crystal structure of PH0725 from Pyrococcus horikoshii OT3 | ||||||
Components | diphthine synthase | ||||||
Keywords | TRANSFERASE / 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 Å | ||||||
Authors | Yamamoto, H. / Matsuura, Y. / Ono, N. / 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. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p6l.cif.gz | 128 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p6l.ent.gz | 98.3 KB | Display | PDB format |
PDBx/mmJSON format | 2p6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2p6l_validation.pdf.gz | 783.5 KB | Display | wwPDB validaton report |
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Full document | 2p6l_full_validation.pdf.gz | 788.6 KB | Display | |
Data in XML | 2p6l_validation.xml.gz | 26.3 KB | Display | |
Data in CIF | 2p6l_validation.cif.gz | 39.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/2p6l ftp://data.pdbj.org/pub/pdb/validation_reports/p6/2p6l | HTTPS FTP |
-Related structure data
Related structure data | 2e8hC 2hr8C 2huqC 2hutC 2huvC 2huxC 2owfC 2owgC 2owkC 2owuC 2owvC 2p2xC 2p5cC 2p5fC 2p6dC 2p6iC 2p6kC 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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2 |
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Unit cell |
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Details | Biological assembly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 29581.389 Da / Num. of mol.: 2 / Mutation: Y220M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / 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: 3.24 Å3/Da / Density % sol: 62.02 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 5.5 Details: 3.85M Sodium formate, 0.1M Sodium acetate, pH 5.5, MICROBATCH, temperature 291K |
-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: Nov 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 53231 / Num. obs: 53231 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 27.375 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.06 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5211 / Rsym value: 0.182 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1WNG Resolution: 2→29.94 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 30.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→29.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012
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