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Yorodumi- PDB-5tro: 1.8 Angstrom Resolution Crystal Structure of Dimerization and Tra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tro | ||||||
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Title | 1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus. | ||||||
Components | Penicillin-binding protein 1 | ||||||
Keywords | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Dimerization Domain / Transpeptidase Domain / Penicillin-Binding Protein 1 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.8 Angstrom Resolution Crystal Structure of Dimerization and Transpeptidase domains (residues 39-608) of Penicillin-Binding Protein 1 from Staphylococcus aureus. Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / 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 | 5tro.cif.gz | 421.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tro.ent.gz | 356.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tro.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/5tro ftp://data.pdbj.org/pub/pdb/validation_reports/tr/5tro | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 64810.695 Da / Num. of mol.: 2 / Fragment: UNP residues 39-608 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria) Strain: COL / Gene: pbp1, SACOL1194 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: A0A0H2WVW5 #2: Chemical | #3: 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: 2.11 Å3/Da / Density % sol: 41.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Protein: 10.8 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), Screen: JCSG+ (A5), 0.2M Magnesium formate, 20% (w/v) PEG 3350. |
-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 300 mm CCD / Detector: CCD / Date: Oct 20, 2016 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 98204 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.793 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→29.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.435 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.118 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.7 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→29.59 Å
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