+Open data
-Basic information
Entry | Database: PDB / ID: 6xbe | ||||||
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Title | Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-1F | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Cyclic peptide / macrocycle inhibitor / ANTIBIOTIC / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase activity / beta-lactamase / Inhibitor, Cyclic peptide / Metallo-beta-lactamase type 2 Function and homology information | ||||||
Biological species | Klebsiella pneumoniae (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Worrall, L.J. / Sun, T. / Mulligan, V.K. / Strynadka, N.C.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Computationally designed peptide macrocycle inhibitors of New Delhi metallo-beta-lactamase 1. Authors: Mulligan, V.K. / Workman, S. / Sun, T. / Rettie, S. / Li, X. / Worrall, L.J. / Craven, T.W. / King, D.T. / Hosseinzadeh, P. / Watkins, A.M. / Renfrew, P.D. / Guffy, S. / Labonte, J.W. / ...Authors: Mulligan, V.K. / Workman, S. / Sun, T. / Rettie, S. / Li, X. / Worrall, L.J. / Craven, T.W. / King, D.T. / Hosseinzadeh, P. / Watkins, A.M. / Renfrew, P.D. / Guffy, S. / Labonte, J.W. / Moretti, R. / Bonneau, R. / Strynadka, N.C.J. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xbe.cif.gz | 203 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xbe.ent.gz | 158.5 KB | Display | PDB format |
PDBx/mmJSON format | 6xbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xb/6xbe ftp://data.pdbj.org/pub/pdb/validation_reports/xb/6xbe | HTTPS FTP |
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-Related structure data
Related structure data | 6xbfC 6xciC 4exsS 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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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 26273.607 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: NDM-1, bla NDM-1, blaNDM-1, blaNDM1 / Production host: Escherichia coli (E. coli) / References: UniProt: E9NWK5 #2: Protein/peptide | #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 25% (w/v) PEG 2000 monomethyl ether, 0.1M MES, pH 6.5 and 200mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 23, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→46.76 Å / Num. obs: 72645 / % possible obs: 89.5 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.052 / Rrim(I) all: 0.079 / Net I/σ(I): 6.7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4exs Resolution: 1.8→46.76 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.888 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 155.94 Å2 / Biso mean: 35.189 Å2 / Biso min: 15.68 Å2
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Refinement step | Cycle: final / Resolution: 1.8→46.76 Å
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Refine LS restraints | Type: r_bond_refined_d / Dev ideal: 0.007 / Dev ideal target: 0.013 / Number: 7238 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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