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- PDB-2ex2: Crystal structure of penicillin binding protein 4 (dacB) from Esc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ex2 | ||||||
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Title | Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli | ||||||
![]() | Penicillin-binding protein 4 | ||||||
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Function / homology | ![]() serine-type carboxypeptidase activity / peptidoglycan metabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kishida, H. / Unzai, S. / Roper, D.I. / Lloyd, A. / Park, S.-Y. / Tame, J.R.H. | ||||||
![]() | ![]() Title: Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics Authors: Kishida, H. / Unzai, S. / Roper, D.I. / Lloyd, A. / Park, S.-Y. / Tame, J.R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.6 KB | Display | ![]() |
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PDB format | ![]() | 83 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49796.711 Da / Num. of mol.: 1 / Mutation: D261Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P24228, ![]() ![]() |
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#2: Chemical | ChemComp-GOL / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.7 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2005 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.55→50 Å / Num. obs: 75038 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.364 / % possible all: 77.8 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.447 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.591 Å / Total num. of bins used: 20
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