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Yorodumi- PDB-5dvy: 2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dvy | ||||||
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Title | 2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium | ||||||
Components | Penicillin binding protein 2 prime | ||||||
Keywords | PENICILLIN-BINDING PROTEIN / penicillin binding protein 2 prime / PBP2 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterococcus faecium DO (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å | ||||||
Authors | Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Filippova, E. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium. Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Filippova, E. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dvy.cif.gz | 266.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dvy.ent.gz | 223.2 KB | Display | PDB format |
PDBx/mmJSON format | 5dvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/5dvy ftp://data.pdbj.org/pub/pdb/validation_reports/dv/5dvy | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 71032.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium DO (bacteria) / Strain: DO / Gene: pbp5, HMPREF0351_11456 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q3XZN6 | ||
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#2: Chemical | ChemComp-TRS / | ||
#3: Chemical | ChemComp-SO4 / #4: 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: 5.82 Å3/Da / Density % sol: 78.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 12.4 mg/ml, 0.01M Tris-HCL (pH 8.3), Screen: Classics II (A3), 0.1M Bis-Tris (pH 5.5), 2M Ammonium sulfate, Cryo: 25% Sucrose, 2M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2015 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→30 Å / Num. obs: 36548 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 68.2 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.95→29.91 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 14.762 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.218 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.27 Å2
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Refinement step | Cycle: 1 / Resolution: 2.95→29.91 Å
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