+Open data
-Basic information
Entry | Database: PDB / ID: 5hla | ||||||||||||||||||
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Title | E. coli PBP1b in complex with acyl-cephalexin and moenomycin | ||||||||||||||||||
Components | Penicillin-binding protein 1B | ||||||||||||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / penicillin-binding protein / inhibitor complex / transpeptidase / transglycosylase / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||||||||||||||
Function / homology | Function and homology information positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape ...positive regulation of bipolar cell growth / cell wall repair / peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / peptidoglycan-based cell wall / regulation of cell shape / outer membrane-bounded periplasmic space / response to antibiotic / proteolysis / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Escherichia coli (E. coli) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||||||||||||||
Authors | King, D.T. / Strynadka, N.C.J. | ||||||||||||||||||
Funding support | Canada, United States, 5items
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Citation | Journal: J. Biol. Chem. / Year: 2016 Title: Escherichia coli Penicillin-Binding Protein 1B: Structural Insights into Inhibition. Authors: King, D.T. / Wasney, G.A. / Nosella, M. / Fong, A. / Strynadka, N.C. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hla.cif.gz | 164.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hla.ent.gz | 123.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hla.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hla_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5hla_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5hla_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 5hla_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/5hla ftp://data.pdbj.org/pub/pdb/validation_reports/hl/5hla | HTTPS FTP |
-Related structure data
Related structure data | 5hl9C 5hlbC 5hldC 3vmaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 83280.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: mrcB, pbpF, ponB, b0149, JW0145 / Production host: Escherichia coli (E. coli) References: UniProt: P02919, peptidoglycan glycosyltransferase, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Chemical | ChemComp-63U / ( |
#3: Chemical | ChemComp-M0E / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.57 Å3/Da / Density % sol: 65.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Drops contained 1uL of protein solution (20mg/mL protein, 100uM moenomycin and 2mM cephalexin) mixed with an equal volume of precipitant (20% w/v PEG 3350, 0.2M potassium/sodium tartate, 0.1M Bis Tris pH 8.5). |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Feb 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→63.76 Å / Num. obs: 49407 / % possible obs: 98.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 42.47 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.36→2.42 Å / Rmerge(I) obs: 0.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VMA Resolution: 2.36→62.35 Å / Cor.coef. Fo:Fc: 0.8545 / Cor.coef. Fo:Fc free: 0.8556 / SU R Cruickshank DPI: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.269 / SU Rfree Blow DPI: 0.201 / SU Rfree Cruickshank DPI: 0.201
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Displacement parameters | Biso mean: 60.79 Å2
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Refine analyze | Luzzati coordinate error obs: 0.406 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.36→62.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.36→2.42 Å / Total num. of bins used: 20
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