+Open data
-Basic information
Entry | Database: PDB / ID: 5lvt | |||||||||
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Title | Structure of HU protein from Lactococcus lactis | |||||||||
Components | DNA-binding protein HU | |||||||||
Keywords | DNA BINDING PROTEIN / HU PROTEIN / DNA BINDING / LACTOCOCCUS LACTIS | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Lactococcus lactis subsp. lactis (lactic acid bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Le Meur, R. / Coste, F. / Castaing, B. | |||||||||
Citation | Journal: To Be Published Title: Structure of HU protein from Lactococcus lactis Authors: Le Meur, R. / Coste, F. / Castaing, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lvt.cif.gz | 149.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lvt.ent.gz | 119.1 KB | Display | PDB format |
PDBx/mmJSON format | 5lvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/5lvt ftp://data.pdbj.org/pub/pdb/validation_reports/lv/5lvt | HTTPS FTP |
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-Related structure data
Related structure data | 1mulS S: Starting model for refinement |
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Similar structure data |
-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
#1: Protein | Mass: 9692.154 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (lactic acid bacteria) Strain: IL1403 / Gene: hup, hslA, LL0502, L102317 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CI64 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 100mM Na acetate, 2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.03 Å / Num. obs: 22969 / % possible obs: 97.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.593 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MUL Resolution: 2.1→43.03 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.157
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Displacement parameters | Biso mean: 47.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→43.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
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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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