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- PDB-1zs3: The crystal structure of the Lactococcus lactis MG1363 DpsB protein -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zs3 | ||||||
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Title | The crystal structure of the Lactococcus lactis MG1363 DpsB protein | ||||||
![]() | Lactococcus lactis MG1363 DpsA | ||||||
![]() | DNA BINDING PROTEIN / Oxidative stress / Dps / DNA binding / Lactic acid bacteria | ||||||
Function / homology | Ferritin, core subunit, four-helix bundle / Ferritin / Up-down Bundle / Mainly Alpha![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stillman, T.J. / Upadhyay, M. / Norte, V.A. / Sedelnikova, S.E. / Carradus, M. / Tzokov, S. / Bullough, P.A. / Shearman, C.A. / Gasson, M.J. / Williams, C.H. ...Stillman, T.J. / Upadhyay, M. / Norte, V.A. / Sedelnikova, S.E. / Carradus, M. / Tzokov, S. / Bullough, P.A. / Shearman, C.A. / Gasson, M.J. / Williams, C.H. / Artymiuk, P.J. / Green, J. | ||||||
![]() | ![]() Title: The crystal structures of Lactococcus lactis MG1363 Dps proteins reveal the presence of an N-terminal helix that is required for DNA binding. Authors: Stillman, T.J. / Upadhyay, M. / Norte, V.A. / Sedelnikova, S.E. / Carradus, M. / Tzokov, S. / Bullough, P.A. / Shearman, C.A. / Gasson, M.J. / Williams, C.H. / Artymiuk, P.J. / Green, J. #1: Journal: Mol.Microbiol. / Year: 1999 Title: Two operons that encode FNR-like proteins in Lactococcus lactis Authors: Gostick, D.O. / Griffin, H.G. / Shearman, C.A. / Scott, C. / Green, J. / Gasson, M.J. / Guest, J.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 402.3 KB | Display | ![]() |
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PDB format | ![]() | 335.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.5 KB | Display | ![]() |
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Full document | ![]() | 490.8 KB | Display | |
Data in XML | ![]() | 40 KB | Display | |
Data in CIF | ![]() | 62.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1zujC ![]() 1qghS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The 12 subunits in the asymmetric unit form the biological assembly, a dodecamer with 23 symmetry. |
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Components
#1: Protein | Mass: 21011.783 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: flpB / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 57.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2.0M Sodium Formate, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.7→15 Å / Num. all: 85912 / Num. obs: 85912 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 61.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 7.5 | ||||||||||||||||||
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.7 / Num. unique all: 12388 / Rsym value: 0.407 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1qgh Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.166 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.755 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.165 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20 /
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