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- PDB-1mpl: CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mpl | ||||||
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Title | CRYSTAL STRUCTURE OF PHOSPHONATE-INHIBITED D-ALA-D-ALA PEPTIDASE REVEALS AN ANALOG OF A TETRAHEDRAL TRANSITION STATE | ||||||
![]() | D-alanyl-D-alanine carboxypeptidase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Silvaggi, N.R. / Anderson, J.W. / Brinsmade, S.R. / Pratt, R.F. / Kelly, J.A. | ||||||
![]() | ![]() Title: The Crystal 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. #1: ![]() 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. #2: ![]() Title: The Refined Crystallographic Structure of a Dd-Peptidase Penicillin-Target Enzyme at 1.6 A Resolution Authors: Kelly, J.A. / Kuzin, A.P. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.2 KB | Display | ![]() |
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PDB format | ![]() | 132.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3pteS S: Starting model for refinement |
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Similar 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: 37422.574 Da / Num. of mol.: 1 / Fragment: DD-Peptidase / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P15555, ![]() | ||
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#2: Chemical | ChemComp-RE1 / | ||
#3: Chemical | ChemComp-GOL / ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 45.8 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: PEG 8000, SODIUM PHOSPHATE, pH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 16, 2001 / Details: MIRRORS | |||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.12→50 Å / Num. all: 701505 / Num. obs: 127013 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 27.2 | |||||||||
Reflection shell | Resolution: 1.12→1.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3 / % possible all: 75.1 | |||||||||
Reflection | *PLUS Num. measured all: 701505 | |||||||||
Reflection shell | *PLUS % possible obs: 75.1 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3PTE Resolution: 1.12→10 Å / Num. parameters: 28853 / Num. restraintsaints: 36144 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.029
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Refine analyze | Num. disordered residues: 24 / Occupancy sum hydrogen: 225 / Occupancy sum non hydrogen: 3081.77 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 9999 Å / Num. reflection Rfree: 6242 / Rfactor Rfree![]() ![]() | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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