+Open data
-Basic information
Entry | Database: PDB / ID: 2p6o | ||||||
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Title | Crystal 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 / DIFFERENCE FOURIER / Resolution: 1.65 Å | ||||||
Authors | Yamamoto, H. / Taketa, M. / Tanaka, Y. / Matsuura, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of TTHB049 from Thermus thermophilus HB8 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 | 2p6o.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p6o.ent.gz | 65.8 KB | Display | PDB format |
PDBx/mmJSON format | 2p6o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/2p6o ftp://data.pdbj.org/pub/pdb/validation_reports/p6/2p6o | HTTPS FTP |
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-Related structure data
Related structure data | 2hiaC 2owdC 2oweC 2p2yC 2p2zC 2p30C 2p6mC 2p75C 2p77C 2p78C 2p79C 2p9fC 2p9yC 2p9zC 2pa0C 1v37S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Biological assembly is a monomer; the asymmetric unit contains the two biological units. |
-Components
#1: Protein | Mass: 19646.504 Da / Num. of mol.: 2 / Mutation: L12T 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: 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: 2.72 Å3/Da / Density % sol: 54.81 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 8.3 Details: 2.75M Sodium chloride, 0.1M Tris, pH 8.3, 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 VII / Detector: IMAGE PLATE / Date: Nov 2, 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: 1.65→20 Å / Num. all: 51923 / Num. obs: 51923 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.079 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5147 / Rsym value: 0.395 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1V37 Resolution: 1.65→19.62 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: 22.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→19.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.014
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