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Yorodumi- PDB-2xdm: Crystal structure of a complex between Actinomadura R39 DD peptid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xdm | ||||||
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Title | Crystal structure of a complex between Actinomadura R39 DD peptidase and a peptidoglycan mimetic boronate inhibitor | ||||||
Components | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE | ||||||
Keywords | HYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / BORONIC ACID / PEPTIDOGLYCAN / HYDROLASE | ||||||
Function / homology | Function and homology information 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 | ACTINOMADURA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Rocaboy, M. / Sauvage, E. / Herman, R. / Kerff, F. / Charlier, P. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Crystal Structure of a Complex between the Actinomadura R39 Dd-Peptidase and a Peptidoglycan- Mimetic Boronate Inhibitor: Interpretation of a Transition State Analogue in Terms of Catalytic Mechanism. Authors: Dzhekieva, L. / Rocaboy, M. / Kerff, F. / Charlier, P. / Sauvage, E. / Pratt, R.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xdm.cif.gz | 672.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xdm.ent.gz | 562.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xdm_validation.pdf.gz | 988 KB | Display | wwPDB validaton report |
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Full document | 2xdm_full_validation.pdf.gz | 1009.2 KB | Display | |
Data in XML | 2xdm_validation.xml.gz | 68.8 KB | Display | |
Data in CIF | 2xdm_validation.cif.gz | 96.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/2xdm ftp://data.pdbj.org/pub/pdb/validation_reports/xd/2xdm | HTTPS FTP |
-Related structure data
Related structure data | 2wk0S 2wix S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 47647.004 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ACTINOMADURA (bacteria) / Strain: R39 References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase |
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-Non-polymers , 5 types, 582 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CO / #4: Chemical | #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.5 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97969 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97969 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→33 Å / Num. obs: 77588 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.6 / % possible all: 99.4 |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WK0 Resolution: 2.4→32.43 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 18.546 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
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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: 26.566 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→32.43 Å
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