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Yorodumi- PDB-1zuj: The crystal structure of the Lactococcus lactis MG1363 DpsA protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zuj | ||||||
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Title | The crystal structure of the Lactococcus lactis MG1363 DpsA protein | ||||||
Components | hypothetical protein Llacc01001955 | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
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. ...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. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zuj.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zuj.ent.gz | 117 KB | Display | PDB format |
PDBx/mmJSON format | 1zuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1zuj_validation.pdf.gz | 391.2 KB | Display | wwPDB validaton report |
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Full document | 1zuj_full_validation.pdf.gz | 414.9 KB | Display | |
Data in XML | 1zuj_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 1zuj_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zu/1zuj ftp://data.pdbj.org/pub/pdb/validation_reports/zu/1zuj | HTTPS FTP |
-Related structure data
Related structure data | 1zs3SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dodecamer generated from the tetramer in the asymmetric unit by the operations: 2-y, x-y, z and 2-x+y, 2-x, z. |
-Components
#1: Protein | Mass: 20951.639 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Strain: MG1363 / Gene: flpA / Plasmid: pET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 58.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.7M ammonium sulphate, 0.1M HEPES/Na, pH 7.5, 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: 1.488 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2.9→15 Å / Num. all: 22949 / Num. obs: 22949 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 77.4 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 6.7 | ||||||||||||||||||
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3298 / Rsym value: 0.382 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ZS3 Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.839 / SU B: 21.27 / SU ML: 0.393 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.524 / 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: 53.953 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.974 Å / Total num. of bins used: 20 /
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