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- PDB-1pw8: Covalent Acyl Enzyme Complex Of The R61 DD-Peptidase with A Highl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1pw8 | ||||||
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Title | Covalent Acyl Enzyme Complex Of The R61 DD-Peptidase with A Highly Specific Cephalosporin | ||||||
![]() | D-alanyl-D-alanine carboxypeptidase![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Silvaggi, N.R. / Josephine, H.R. / Pratt, R.F. / Kelly, J.A. | ||||||
![]() | ![]() Title: Crystal structures of complexes between the R61 DD-peptidase and peptidoglycan-mimetic beta-lactams: a non-covalent complex with a "perfect penicillin" Authors: Silvaggi, N.R. / Josephine, H.R. / Kuzin, A.P. / Nagarajan, 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: A 1.2-A Snapshot of the Final Step of Bacterial Cell Wall Biosynthesis Authors: Lee, W. / Mcdonough, M.A. / Kotra, L. / Li, Z.H. / Silvaggi, N.R. / Takeda, Y. / Kelly, J.A. / Mobashery, S. #3: ![]() Title: The Refined Crystallographic Structure of a Dd-Peptidase Penicillin-Target Enzyme at 1.6 A Resolution Authors: Kelly, J.A. / Kuzin, A.P. | ||||||
History |
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Remark 600 | ACYL FORM OF LIGAND H2A The ligand H2A in this structure is in its acylated form. The acylation ...ACYL FORM OF LIGAND H2A The ligand H2A in this structure is in its acylated form. The acylation reaction resulted in the removal of the covalent bond between atoms N5 and C8 of H2A 400, and the formation of the covalent bond between atom OG of SER 62 and atom C8 of H2A 400. MISSING LIGAND H2A ATOMS The following atoms are missing in the coordinate file for ligand CSC 400 in this structure: O1 C1 O2 C26 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.3 KB | Display | ![]() |
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PDB format | ![]() | 130.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1pw1C ![]() 1pwcC ![]() 1pwdC ![]() 1pwgC ![]() 3pteS 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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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-H2A / ( | ||
#3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 44.86 % |
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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 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Apr 12, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.3→50 Å / Num. all: 82877 / Num. obs: 82877 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 81.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3PTE Resolution: 1.3→10 Å / Num. parameters: 28501 / Num. restraintsaints: 34218 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.031
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Refine analyze | Luzzati coordinate error obs: 0.06 Å / Num. disordered residues: 14 / Occupancy sum hydrogen: 243 / Occupancy sum non hydrogen: 3067.42 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
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Refine LS restraints |
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