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Yorodumi- PDB-4r23: Structure of a putative peptidoglycan glycosyltransferase from At... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r23 | ||||||
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Title | Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with dicloxacillin | ||||||
Components | Peptidoglycan glycosyltransferase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / penicillin-binding protein / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 DSM 20469 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Clancy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with dicloxacillin Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Clancy, S. / 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 | 4r23.cif.gz | 325.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r23.ent.gz | 263.6 KB | Display | PDB format |
PDBx/mmJSON format | 4r23.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r23_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4r23_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4r23_validation.xml.gz | 37 KB | Display | |
Data in CIF | 4r23_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/4r23 ftp://data.pdbj.org/pub/pdb/validation_reports/r2/4r23 | HTTPS FTP |
-Related structure data
Related structure data | 4qjgS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 50648.797 Da / Num. of mol.: 2 / Fragment: Residues 505-954 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Atopobium parvulum DSM 20469 (bacteria) Strain: ATCC 33793 / DSM 20469 / JCM 10300 / VPI 0546 / 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: Chemical | ChemComp-P4G / #4: Chemical | ChemComp-EDO / #5: 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: 2.65 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Tri-Sodium Citrate, 0.1 M Tris, 15% PEG400, pH 8.5, 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: Dec 9, 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: 1.84→30 Å / Num. all: 91253 / Num. obs: 91253 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.84→1.87 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / Num. unique all: 4542 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QJG Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.784 / SU ML: 0.082 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.1 / 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: 41.516 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→30 Å
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Refine LS restraints |
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