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Open data
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Basic information
Entry | Database: PDB / ID: 4lqe | ||||||
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Title | Crystal Structure of MepB | ||||||
![]() | MepB | ||||||
![]() | DNA BINDING PROTEIN / Endonuclease | ||||||
Function / homology | MepB-like / MepB-like / MepB-like superfamily / MepB-like / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein / Uncharacterized protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Faham, S. / Agah, S. | ||||||
![]() | ![]() Title: Structural characterization of MepB from Staphylococcus aureus reveals homology to endonucleases. Authors: Agah, S. / Poulos, S. / Banchs, C. / Faham, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.8 KB | Display | ![]() |
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PDB format | ![]() | 59.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.1 KB | Display | ![]() |
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Full document | ![]() | 436.1 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19258.934 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.43 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 100 mM Bis-tris, pH 5.0, 2.3 M NH4SO4, 1% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 12092 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 5 / Num. unique all: 969 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.861 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→23.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 12.719 Å / Origin y: 13.763 Å / Origin z: 66.023 Å
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