+Open data
-Basic information
Entry | Database: PDB / ID: 6ntz | ||||||
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Title | Crystal structure of E. coli PBP5-meropenem | ||||||
Components | D-alanyl-D-alanine carboxypeptidase | ||||||
Keywords | hydrolase/antibiotic / carboxypeptidase / HYDROLASE / hydrolase-hydrolase inhibitor complex / hydrolase-antibiotic complex | ||||||
Function / homology | Function and homology information peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space ...peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / regulation of cell shape / protein homodimerization activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Caveney, N.A. / Strynadka, N.C.J. / Caballero, G. / Worrall, L.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural insight into YcbB-mediated beta-lactam resistance in Escherichia coli. Authors: Caveney, N.A. / Caballero, G. / Voedts, H. / Niciforovic, A. / Worrall, L.J. / Vuckovic, M. / Fonvielle, M. / Hugonnet, J.E. / Arthur, M. / Strynadka, N.C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ntz.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ntz.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 6ntz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ntz_validation.pdf.gz | 787.1 KB | Display | wwPDB validaton report |
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Full document | 6ntz_full_validation.pdf.gz | 791.8 KB | Display | |
Data in XML | 6ntz_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6ntz_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/6ntz ftp://data.pdbj.org/pub/pdb/validation_reports/nt/6ntz | HTTPS FTP |
-Related structure data
Related structure data | 6ntwC 3mzfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 44493.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dacA, EC1094V2_3241, EC3234A_6c00520, EL75_3150 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0A0GRC5, UniProt: P0AEB2*PLUS, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-MXR / ( |
#3: 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: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion / pH: 7 Details: PBP5 protein was crystallized using 0.2 uL protein solution (5 mg/mL purified protein in 20 mM HEPES pH8, 300 mM NaCl) and 1 uL of mother liquor (0.1 M tris pH 7, 7% PEG 400) with the addition of 1 mM meropenem. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 9, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→46.082 Å / Num. obs: 52513 / % possible obs: 99.5 % / Redundancy: 5.725 % / Biso Wilson estimate: 47.53 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.14 / Χ2: 1.273 / Net I/σ(I): 7.27 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MZF Resolution: 2.2→46.082 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→46.082 Å
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Refine LS restraints |
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LS refinement shell |
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