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Yorodumi- PDB-1sde: Toward Better Antibiotics: Crystal Structure Of D-Ala-D-Ala Pepti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sde | ||||||
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Title | Toward Better Antibiotics: Crystal Structure Of D-Ala-D-Ala Peptidase inhibited by a novel bicyclic phosphate inhibitor | ||||||
Components | D-alanyl-D-alanine carboxypeptidase | ||||||
Keywords | HYDROLASE / CYCLIC PHOSPHATE / PEPTIDOGLYCAN / PENICILLIN BINDING PROTEIN / ANTIBIOTIC | ||||||
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 / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å | ||||||
Authors | Silvaggi, N.R. / Kaur, K. / Adediran, S.A. / Pratt, R.F. / Kelly, J.A. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Toward better antibiotics: crystallographic studies of a novel class of DD-peptidase/beta-lactamase inhibitors Authors: Silvaggi, N.R. / Kaur, K. / Adediran, S.A. / Pratt, R.F. / Kelly, J.A. #1: Journal: Biochemistry / Year: 2003 Title: Structure of Phosphonate-Inhibited D-Ala-D-Ala Peptidase Reveals an Analogue of a Tetrahedral Transition State. Authors: Silvaggi, N.R. / Anderson, J.W. / Brinsmade, S.R. / Pratt, R.F. / Kelly, J.A. #2: Journal: J.Mol.Biol. / Year: 2002 Title: STRUCTURES OF TWO KINETIC INTERMEDIATES REVEAL SPECIES SPECIFICITY OF PENICILLIN-BINDING PROTEINS Authors: McDonough, M.A. / Anderson, J.W. / Silvaggi, N.R. / Pratt, R.F. / Knox, J.R. / Kelly, J.A. #3: Journal: J.Mol.Biol. / Year: 1995 Title: THE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILLIN-TARGET ENZYME AT 1.6A RESOLUTION Authors: Kelly, J.A. / Kuzin, A.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sde.cif.gz | 168.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sde.ent.gz | 131.6 KB | Display | PDB format |
PDBx/mmJSON format | 1sde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sde_validation.pdf.gz | 457.2 KB | Display | wwPDB validaton report |
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Full document | 1sde_full_validation.pdf.gz | 459.8 KB | Display | |
Data in XML | 1sde_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 1sde_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/1sde ftp://data.pdbj.org/pub/pdb/validation_reports/sd/1sde | HTTPS FTP |
-Related structure data
Related structure data | 1scwC 3pteS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Monomer is biologically active unit |
-Components
#1: Protein | Mass: 37220.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. (bacteria) / Strain: R61 References: UniProt: P15555, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-2PB / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 20% PEG 8000, 50mM sodium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50 Å / Num. all: 122116 / Num. obs: 119308 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rsym value: 0.056 / Net I/σ(I): 28.8 |
Reflection shell | Resolution: 1.15→1.19 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 9967 / Rsym value: 0.245 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3PTE Resolution: 1.15→10 Å / Num. parameters: 28915 / Num. restraintsaints: 0 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.9%
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Displacement parameters | Biso mean: 9.1 Å2 | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 25 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3069.67 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→10 Å
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Refine LS restraints |
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