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Yorodumi- PDB-3dx5: Crystal structure of the probable 3-DHS dehydratase AsbF involved... -
+Open data
-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 | ||||||
Components | uncharacterized protein AsbF | ||||||
Keywords | 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 | Function and homology information 3-dehydroshikimate dehydratase / 3-dehydroshikimate dehydratase activity / 3,4-dihydroxybenzoate biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å | ||||||
Authors | Kim, Y. / Maltseva, N. / Stols, L. / Eschenfeldt, W. / Pfleger, B.F. / Sherman, D.H. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dx5.cif.gz | 78 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dx5.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dx5_validation.pdf.gz | 468.7 KB | Display | wwPDB validaton report |
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Full document | 3dx5_full_validation.pdf.gz | 473.5 KB | Display | |
Data in XML | 3dx5_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 3dx5_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/3dx5 ftp://data.pdbj.org/pub/pdb/validation_reports/dx/3dx5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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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.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS1843, BA_1986, GBAA1986 / Plasmid: pMCSG26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81RQ4 |
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-Non-polymers , 6 types, 236 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.12→49.4 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.044 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.165 / ESU R Free: 0.138 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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