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- PDB-3d63: Crystal structure of inorganic pyrophosphatase from Burkholderia ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d63 | ||||||
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Title | Crystal structure of inorganic pyrophosphatase from Burkholderia pseudomallei | ||||||
![]() | Inorganic pyrophosphatase | ||||||
![]() | HYDROLASE / structural genomics / SSGCID / pyrophosphatase / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Combining functional and structural genomics to sample the essential Burkholderia structome. Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.3 KB | Display | ![]() |
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PDB format | ![]() | 90.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3dahC ![]() 3eizC ![]() 3ej2C ![]() 3ek2C ![]() 3ezoC ![]() 3f0fC ![]() 3ftpC ![]() 3gk0C ![]() 3gk3C ![]() 3gvfC ![]() 3gwaC ![]() 3gweC ![]() 3imlC ![]() 3sz8C ![]() 3t4cC ![]() 3tmlC ![]() 3tmqC ![]() 3txyC ![]() 3u7jC ![]() 3ue9C ![]() 3uk1C ![]() 3uk2C ![]() 3undC ![]() 3uptC ![]() 3urrC ![]() 3uw1C ![]() 3uw2C ![]() 3uw3C ![]() 3v2iC ![]() 3v7nC ![]() 3v8hC ![]() 3v9oC ![]() 3v9pC ![]() 3vavC ![]() 4ddoC ![]() 4dfeC ![]() 4dheC ![]() 4dhkC ![]() 4dutC ![]() 4dz4C ![]() 4e4tC ![]() 4efiC ![]() 4eg0C ![]() 4egjC ![]() 4ek2C ![]() 4eqyC ![]() 4ewgC ![]() 4exqC ![]() 4f2gC ![]() 4f32C ![]() 4f3nC ![]() 4f3yC ![]() 4f4hC ![]() 4f7dC ![]() 4fk8C ![]() 4fryC ![]() 4g1kC ![]() 4g67C ![]() 4ghkC ![]() 4h3yC ![]() 4h3zC ![]() 4h4gC C: citing same article ( |
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Similar structure data | |
Other databases |
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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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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 4 - 174 / Label seq-ID: 25 - 195
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Components
#1: Protein | Mass: 21473.625 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: N-terminal 6-His tag and 3C protease cleavage. The un-cleaved protein was crystallized. Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | RESIDUES ALA C(-19) TO HIS C(-14) THAT ARE PRESENT IN COORDINATES, ARE THE FRAGMENT OF N-TERMINAL ...RESIDUES ALA C(-19) TO HIS C(-14) THAT ARE PRESENT IN COORDINATE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.86 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 100 mM Potassium phosphate pH 6.7, 49% PEG 200, 12.3 mg/mL Protein, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→61.9 Å / Num. obs: 37853 / % possible obs: 99.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 4.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.527 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→61.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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