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Yorodumi- PDB-3dah: 2.3 A crystal structure of ribose-phosphate pyrophosphokinase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dah | ||||||
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Title | 2.3 A crystal structure of ribose-phosphate pyrophosphokinase from Burkholderia pseudomallei | ||||||
Components | Ribose-phosphate pyrophosphokinase | ||||||
Keywords | TRANSFERASE / BURKHOLDERIA / PSEUDOMALLEI / RIBOSE / PHOSPHATE / PYROPHOSPHOKINASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / Magnesium / Metal binding / Nucleotide biosynthesis | ||||||
Function / homology | Function and homology information ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / ribonucleoside monophosphate biosynthetic process / nucleotide biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / nucleoside metabolic process / kinase activity / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Plos One / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dah.cif.gz | 179 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dah.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 3dah.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3dah ftp://data.pdbj.org/pub/pdb/validation_reports/da/3dah | HTTPS FTP |
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-Related structure data
Related structure data | 3d63C 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 1dkuS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 34335.734 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: prsA, BURPS1710b_0753 / Plasmid: Ava0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q3JW86, UniProt: Q63XL8*PLUS, ribose-phosphate diphosphokinase #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 46.55 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 5.9 Details: 20% PEG 3350, 0.2M Magnesium formate, pH 5.9, VAPOR DIFFUSION, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→50 Å / Num. obs: 41722 / % possible obs: 98 % / Redundancy: 6 % / Rmerge(I) obs: 0.09 / Χ2: 0.926 / Net I/σ(I): 7.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1DKU Resolution: 2.3→46.93 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 8.489 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.367 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 48.513 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→46.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.361 Å / Total num. of bins used: 20
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