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- PDB-3a3e: Crystal structure of penicillin binding protein 4 (dacB) from Hae... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3a3e | ||||||
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Title | Crystal structure of penicillin binding protein 4 (dacB) from Haemophilus influenzae, complexed with novel beta-lactam (CMV) | ||||||
![]() | Penicillin-binding protein 4 | ||||||
![]() | HYDROLASE / Penicillin Binding Protein 4 / PBP4 / dacB | ||||||
Function / homology | ![]() serine-type carboxypeptidase activity / peptidoglycan metabolic process / proteolysis Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kawai, F. / Roper, D.I. / Park, S.-Y. / Tame, J.R.H. | ||||||
![]() | ![]() Title: Crystal structures of penicillin-binding proteins 4 and 5 from Haemophilus influenzae Authors: Kawai, F. / Clarke, T.B. / Roper, D.I. / Han, G.-J. / Hwang, K.Y. / Unzai, S. / Obayashi, E. / 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 | ![]() | 174.9 KB | Display | ![]() |
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PDB format | ![]() | 145 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1020.3 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 38.1 KB | Display | |
Data in CIF | ![]() | 51.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 49789.945 Da / Num. of mol.: 2 / Fragment: UNP residues 28-479 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A8E0K8, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES pH 7.5, 25% (w/v) PEG 6000 and 5% (v/v) glycerol, 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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 42914 / % possible obs: 93.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.061 |
Reflection shell | Resolution: 2.4→2.49 Å / Rmerge(I) obs: 0.285 / % possible all: 61.5 |
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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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.776 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→49.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.463 Å / Total num. of bins used: 20
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