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Yorodumi- PDB-4n1x: Structure of a putative peptidoglycan glycosyltransferase from At... -
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-Basic information
Entry | Database: PDB / ID: 4n1x | ||||||
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Title | Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with penicillin G | ||||||
Components | Peptidoglycan glycosyltransferase | ||||||
Keywords | Transferase/Antibiotic / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Susceptibility to Known Mtb Inhibitors / MTBI / glycosyltransferase / penicillin G / Transferase-Antibiotic Complex / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors | ||||||
Function / homology | Function and homology information lipid-linked peptidoglycan transporter activity / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / cell division site / penicillin binding / regulation of cell shape / cell division / membrane Similarity search - Function | ||||||
Biological species | Atopobium parvulum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI) | ||||||
Citation | Journal: To be Published Title: Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with penicillin G Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Babnigg, G. / Rubin, E. / Sacchettini, J. / Joachimiak, A. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n1x.cif.gz | 329.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n1x.ent.gz | 266 KB | Display | PDB format |
PDBx/mmJSON format | 4n1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n1x_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4n1x_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4n1x_validation.xml.gz | 39.9 KB | Display | |
Data in CIF | 4n1x_validation.cif.gz | 60.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/4n1x ftp://data.pdbj.org/pub/pdb/validation_reports/n1/4n1x | HTTPS FTP |
-Related structure data
Related structure data | 4jbfS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49572.531 Da / Num. of mol.: 2 / Fragment: penicillin-binding domain, UNP residues 515-954 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Atopobium parvulum (bacteria) / Strain: DSM 20469 / Gene: Apar_1344 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic References: UniProt: C8W8H7, peptidoglycan glycosyltransferase #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: 2.78 Å3/Da / Density % sol: 55.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.085 M MES, 10.2% (w/v) PEG 20000, 10 % (w/v) Glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-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: Aug 20, 2013 / Details: Beryllium lenses |
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→30 Å / Num. all: 70573 / Num. obs: 70573 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 9.2 / % possible all: 99.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JBF Resolution: 2→29.93 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.245 / SU ML: 0.122 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.157 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.239 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.93 Å
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