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- PDB-3dx5: Crystal structure of the probable 3-DHS dehydratase AsbF involved... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dx5 | ||||||
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Title | Crystal structure of the probable 3-DHS dehydratase AsbF involved in the petrobactin synthesis from Bacillus anthracis | ||||||
![]() | uncharacterized protein AsbF | ||||||
![]() | LYASE / beta-alpha barrel / petrobactin synthesis / Asb locus / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / unknown function | ||||||
Function / homology | ![]() 3-dehydroshikimate dehydratase / 3-dehydroshikimate dehydratase activity / 3,4-dihydroxybenzoate biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Maltseva, N. / Stols, L. / Eschenfeldt, W. / Pfleger, B.F. / Sherman, D.H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Structural and functional analysis of AsbF: origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis. Authors: Pfleger, B.F. / Kim, Y. / Nusca, T.D. / Maltseva, N. / Lee, J.Y. / Rath, C.M. / Scaglione, J.B. / Janes, B.K. / Anderson, E.C. / Bergman, N.H. / Hanna, P.C. / Joachimiak, A. / Sherman, D.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 78 KB | Display | ![]() |
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PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.7 KB | Display | ![]() |
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Full document | ![]() | 473.5 KB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 23.4 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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1 | ![]()
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2 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33745.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal His-tag with TEV protease cleavage site / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 236 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DHB.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/DHB.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-DHB / |
#5: Chemical | ChemComp-TRS / |
#6: Chemical | ChemComp-GOL / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris pH8.5, 3.2 M soudium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2008 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→49.4 Å / Num. all: 22726 / Num. obs: 22726 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.144 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.11→2.19 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.534 / Mean I/σ(I) obs: 6.7 / Num. unique all: 2210 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: 16.061 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→49.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.175 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 65.6262 Å / Origin y: 70.4113 Å / Origin z: 2.1516 Å
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