+Open data
-Basic information
Entry | Database: PDB / ID: 2enu | ||||||
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Title | Mutant L121M structure of TTHB049 from Thermus thermophilus HB8 | ||||||
Components | Alpha-ribazole-5'-phosphate phosphatase | ||||||
Keywords | HYDROLASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Shimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Mutant L121M structure of TTHB049 from Thermus thermophilus HB8 Authors: Shimizu, K. / Matsuura, Y. / Ono, N. / 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 | 2enu.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2enu.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 2enu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/2enu ftp://data.pdbj.org/pub/pdb/validation_reports/en/2enu | HTTPS FTP |
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-Related structure data
Related structure data | 1v37S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 19646.504 Da / Num. of mol.: 2 / Mutation: L121M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q53WB3, adenosylcobalamin/alpha-ribazole phosphatase #2: Chemical | #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: 2.75 Å3/Da / Density % sol: 55.29 % |
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Crystal grow | Temperature: 295 K / Method: microbatch / pH: 8.3 Details: 2.75M Na Chlor, 0.1M Tris, pH 8.3, Microbatch, 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: Jan 9, 2007 / 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: 1.7→20 Å / Num. all: 47924 / Num. obs: 47924 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.047 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 8.1 / Rsym value: 0.18 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1V37 Resolution: 1.7→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2075248.23 / 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: 52.3941 Å2 / ksol: 0.374365 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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