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- PDB-2gta: Crystal Structure of the putative pyrophosphatase YPJD from Bacil... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2gta | ||||||
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Title | Crystal Structure of the putative pyrophosphatase YPJD from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR428. | ||||||
![]() | Hypothetical protein ypjD | ||||||
![]() | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pyrophosphatase / YPJD / NESG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium | ||||||
Function / homology | NTP pyrophosphohydrolase MazG-related, YpjD / NTP pyrophosphohydrolase MazG, putative catalytic core / MazG nucleotide pyrophosphohydrolase domain / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Uncharacterized protein YpjD![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S.M. / Zhou, W. / Seetharaman, J. / Wang, D. / Ma, L.C. / Acton, T. / Xio, R. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Crystal Structure of the putative pyrophosphatase YPJD from Bacillus subtilis. Authors: Vorobiev, S.M. / Zhou, W. / Seetharaman, J. / Wang, D. / Ma, L.C. / Acton, T. / Xio, R. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.3 KB | Display | ![]() |
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PDB format | ![]() | 68 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.7 KB | Display | ![]() |
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Full document | ![]() | 441.6 KB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | Tetramer according to aggregation screen |
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Components
#1: Protein | Mass: 14345.229 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NA / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 16% PEG 3350, 0.25 M Sodium Tartrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 24876 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 99.3 Å2 / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 2.9→3.02 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.318 / Num. unique all: 2813 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 17.7289 Å2 / ksol: 0.290399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→29.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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