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- PDB-1jrk: Crystal Structure of a Nudix Protein from Pyrobaculum aerophilum ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jrk | ||||||
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Title | Crystal Structure of a Nudix Protein from Pyrobaculum aerophilum Reveals a Dimer with Intertwined Beta Sheets | ||||||
![]() | Nudix homolog | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Nudix/mutT-like fold / mixed alpha/beta / tetramerization due to Hix6x tag / putative Nudix hydrolase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wang, S. / Mura, C. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. | ||||||
![]() | ![]() Title: Structure of a Nudix protein from Pyrobaculum aerophilum reveals a dimer with two intersubunit beta-sheets. Authors: Wang, S. / Mura, C. / Sawaya, M.R. / Cascio, D. / Eisenberg, D. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The putative biologically-relevant assembly is a dimer, and two of these associate to form a weak tetramer in the asymmetric unit. Chains A+B and C+D form the two dimers. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129 KB | Display | ![]() |
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PDB format | ![]() | 104.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.2 KB | Display | ![]() |
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Full document | ![]() | 487.8 KB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 36.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Details | The putative biologically-relevant assembly is a dimer, and two of these associate to form a tetramer in the asymmetric unit. Chains A+B and C+D form the two dimers. |
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Components
#1: Protein | Mass: 17813.570 Da / Num. of mol.: 4 / Mutation: M16L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-MPD / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.63 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: Tris, MPD, MES buffer, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 21, 2001 / Details: mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→90 Å / Num. all: 23707 / Num. obs: 23707 / % possible obs: 98.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 3 / Num. unique all: 2324 / % possible all: 97 |
Reflection | *PLUS Lowest resolution: 90 Å / Num. measured all: 84048 / Rmerge(I) obs: 0.093 |
Reflection shell | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.465 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: P. aerophilum mutT dimer solved in another space group (P21) by Wang et al. Resolution: 2.4→20 Å Isotropic thermal model: restrained isotropic temperature factors Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 33.4 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 8 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.346 / Rfactor Rwork: 0.247 |