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- PDB-3k2x: Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k2x | ||||||
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Title | Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei in complex with 5'-iodo-cytosine | ||||||
![]() | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei. Authors: Begley, D.W. / Hartley, R.C. / Davies, D.R. / Edwards, T.E. / Leonard, J.T. / Abendroth, J. / Burris, C.A. / Bhandari, J. / Myler, P.J. / Staker, B.L. / Stewart, L.J. #1: ![]() 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 | ![]() | 106.5 KB | Display | ![]() |
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PDB format | ![]() | 81.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3f0dC ![]() 3f0eC ![]() 3f0gC ![]() 3ieqC ![]() 3iewC ![]() 3ikeC ![]() 3ikfC ![]() 3jvhC ![]() 3k14C ![]() 3mbmC ![]() 3p0zC ![]() 3p10C ![]() 3qhdC 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | ![]() Mass: 19487.109 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q3JRA0, ![]() |
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-Non-polymers , 5 types, 261 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/I5A.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/I5A.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | ![]() #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.38 % |
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Crystal grow![]() | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 20% PEG 3350, 0.2 M magnesium formate, 34.4 mg/mL protein, 5 mM 5'-iodo-cytosine soak for 5 days, crystal tracking ID 205278a4, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.85→50 Å / Num. obs: 39427 / % possible obs: 98.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.078 / Χ2: 1.059 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.29 / Num. unique all: 3606 / Χ2: 1.299 / % possible all: 90.8 |
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Processing
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Refinement | Method to determine structure![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.55 Å2 / Biso mean: 17.788 Å2 / Biso min: 7.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→27.18 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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