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Open data
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Basic information
Entry | Database: PDB / ID: 1cef | |||||||||
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Title | CEFOTAXIME COMPLEXED WITH THE STREPTOMYCES R61 DD-PEPTIDASE | |||||||||
![]() | D-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE | |||||||||
![]() | HYDROLASE-TRANSPEPTIDASE / D-AMINO ACID PEPTIDASE / PENICILLIN TARGET | |||||||||
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 / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Knox, J.R. / Kuzin, A.P. | |||||||||
![]() | ![]() Title: Binding of cephalothin and cefotaxime to D-ala-D-ala-peptidase reveals a functional basis of a natural mutation in a low-affinity penicillin-binding protein and in extended-spectrum beta-lactamases. Authors: Kuzin, A.P. / Liu, H. / Kelly, J.A. / Knox, J.R. #1: ![]() Title: The Refined Crystallographic Structure of a Dd-Peptidase Penicillin-Target Enzyme at 1.6 A Resolution Authors: Kelly, J.A. / Kuzin, A.P. #2: ![]() Title: Crystallographic Mapping of Beta-Lactams Bound to a D-Alanyl-D-Alanine Peptidase Target Enzyme Authors: Kelly, J.A. / Knox, J.R. / Zhao, H. / Frere, J.M. / Ghaysen, J.M. #3: Journal: Science / Year: 1986 Title: On the origin of bacterial resistance to penicillin: comparison of a beta-lactamase and a penicillin target. Authors: Kelly, J.A. / Dideberg, O. / Charlier, P. / Wery, J.P. / Libert, M. / Moews, P.C. / Knox, J.R. / Duez, C. / Fraipont, C. / Joris, B. #4: ![]() Title: 2.8-A Structure of Penicillin-Sensitive D-Alanyl Carboxypeptidase-Transpeptidase from Streptomyces R61 and Complexes with Beta-Lactams Authors: Kelly, J.A. / Knox, J.R. / Moews, P.C. / Hite, G.J. / Bartolone, J.B. / Zhao, H. / Joris, B. / Frere, J.M. / Ghuysen, J.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.8 KB | Display | ![]() |
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PDB format | ![]() | 60.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.2 KB | Display | ![]() |
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Full document | ![]() | 459.7 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 37422.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P15555, serine-type D-Ala-D-Ala carboxypeptidase |
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#2: Chemical | ChemComp-CEF / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.11 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 29, 1989 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 19106 / % possible obs: 67 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.057 |
Reflection | *PLUS Highest resolution: 2.04 Å / Num. measured all: 38280 |
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Processing
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Refinement | Resolution: 2.04→20 Å / σ(F): 3 Details: SEE STRUCTURE OF NATIVE FOR MULTIPLE CONFORMATIONS (J.A.KELLY AND A.P.KUZIN JOURNAL OF MOLECULAR BIOLOGY, 1995, SUBMITTED).
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Displacement parameters | Biso mean: 6.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→20 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.8 |