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- PDB-2vgk: Crystal structure of Actinomadura R39 DD-peptidase complexed with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vgk | ||||||
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Title | Crystal structure of Actinomadura R39 DD-peptidase complexed with a peptidoglycan-mimetic cephalosporin | ||||||
![]() | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE | ||||||
![]() | HYDROLASE / CELL WALL BIOGENESIS/DEGRADATION / ANTIBIOTIC RESISTANCE / PEPTIDOGLYCAN SYNTHESIS / PROTEASE / SECRETED / CELL SHAPE / CARBOXYPEPTIDASE / PENICILLIN-BINDING / ACTINOMADURA / PEPTIDOGLYCAN / TRANSPEPTIDASE | ||||||
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 | ![]() ![]() | ||||||
![]() | Sauvage, E. / kerff, F. / Herman, R. / Charlier, P. | ||||||
![]() | ![]() Title: Crystal Structures of Complexes of Bacterial Dd-Peptidases with Peptidoglycan-Mimetic Ligands: The Substrate Specificity Puzzle. Authors: Sauvage, E. / Powell, A.J. / Heilemann, J. / Josephin, H.R. / Charlier, P. / Davies, C. / Pratt, R.F. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 346.4 KB | Display | ![]() |
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PDB format | ![]() | 282.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2vgjC ![]() 3bebC ![]() 3becC ![]() 1w79S 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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1 | ![]()
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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: 50083.812 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | #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: 2.71 Å3/Da / Density % sol: 54.3 % / Description: NONE |
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Crystal grow | pH: 8 / Details: pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 99513 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.25→2.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.3 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W79 Resolution: 2.25→15.71 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.867 / SU B: 9.762 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.253 / 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: 26.41 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→15.71 Å
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Refine LS restraints |
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