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- PDB-4b4x: Crystal structure of a complex between Actinomadura R39 DD-peptid... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b4x | ||||||
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Title | Crystal structure of a complex between Actinomadura R39 DD-peptidase and a sulfonamide boronate inhibitor | ||||||
![]() | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE | ||||||
![]() | HYDROLASE / PEPTIDOGLYCAN | ||||||
Function / homology | ![]() serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cannella, S.E. / Sauvage, E. / Herman, R. / Kerff, F. / Rocaboy, M. / Charlier, P. | ||||||
![]() | ![]() Title: Crystal Structure of a Complex between Actinomadura R39 Dd-Peptidase and a Boronate Inhibitor Authors: Sauvage, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 343.5 KB | Display | ![]() |
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PDB format | ![]() | 281.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4b4zC ![]() 1w8qS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47647.004 Da / Num. of mol.: 4 / Fragment: RESIDUES 50-515 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | ChemComp-HQZ / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.41 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→35.64 Å / Num. obs: 55993 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.65→2.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W8Q Resolution: 2.65→35.13 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.889 / SU B: 13.786 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 49.898 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→35.13 Å
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Refine LS restraints |
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