+Open data
-Basic information
Entry | Database: PDB / ID: 2eeq | ||||||
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Title | Mutant Y29M 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Shimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Mutant Y29M structure of PH0725 from Pyrococcus horikoshii OT3 Authors: Shimizu, K. / Ono, N. / Taketa, M. / Nakamoto, T. / Kunishima, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eeq.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eeq.ent.gz | 94.3 KB | Display | PDB format |
PDBx/mmJSON format | 2eeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2eeq_validation.pdf.gz | 798 KB | Display | wwPDB validaton report |
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Full document | 2eeq_full_validation.pdf.gz | 802.9 KB | Display | |
Data in XML | 2eeq_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 2eeq_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ee/2eeq ftp://data.pdbj.org/pub/pdb/validation_reports/ee/2eeq | HTTPS FTP |
-Related structure data
Related structure data | 1wngS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 29581.389 Da / Num. of mol.: 2 / Mutation: Y29M 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-SO4 / #3: Chemical | ChemComp-SAH / | #4: Chemical | #5: 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: 3.16 Å3/Da / Density % sol: 61.11 % |
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Crystal grow | Temperature: 295 K / Method: microbach / pH: 6.5 Details: 1.8M Ammonium Sulfate, 0.1M MES, 0.01M Co Chloride, 1mM DTT, pH 6.5, Microbach, temperature 295K |
-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: Sep 22, 2006 / Details: Mirror |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→15 Å / Num. all: 26782 / Num. obs: 26782 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 54.3 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.095 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.425 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1WNG Resolution: 2.5→14.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1968715.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.5539 Å2 / ksol: 0.367921 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→14.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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