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- PDB-6tix: Crystal structure of penicillin-binding protein 2 from Yersinia p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tix | ||||||
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Title | Crystal structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam | ||||||
![]() | Peptidoglycan D,D-transpeptidase MrdA | ||||||
![]() | MEMBRANE PROTEIN / Class B PBP / Yersinia pestis / HMM transpeptidase / periplasmic protein / peptidoglycan crosslinking / mecillinam | ||||||
Function / homology | ![]() serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pankov, G. / Hunter, W.N. / Dawson, A. | ||||||
![]() | ![]() Title: The structure of penicillin-binding protein 2 from Yersinia pestis in complex with mecillinam Authors: Pankov, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 223.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 52.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lp4S S: Starting model for refinement |
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Similar structure data |
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Links
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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 domain: (Details: Chains AAA BBB) |
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Components
#1: Protein | Mass: 65552.883 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A384KFW3, UniProt: A0A5P8YJF3*PLUS, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % / Description: Branched rectangular prisms |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M ...Details: Crystals were grown in a condition containing 1 uL of 0.8 mg/mL YpPBP2 (in 20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM mecillinam) and 1 uL of reservoir solution (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000). The size of these crystals was optimised by three rounds of macroseeding into condition containing (0.45 M Na+/K+ tartrate, 0.1 M HEPES-NaOH pH 7.5, 7.2% PEG 4000 and 2 mM mecillinam) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→45.693 Å / Num. obs: 27215 / % possible obs: 92.9 % / Redundancy: 2.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.097 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4118 / CC1/2: 0.677 / Rpim(I) all: 0.452 / Rrim(I) all: 0.64 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LP4 Resolution: 2.8→45.693 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.214 / SU B: 29.964 / SU ML: 0.529 / Average fsc free: 0.7294 / Average fsc work: 0.772 / Cross valid method: FREE R-VALUE / ESU R Free: 0.48 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.303 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→45.693 Å
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Refine LS restraints |
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LS refinement shell |
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