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Yorodumi- PDB-1pwg: Covalent Penicilloyl Acyl Enzyme Complex Of The Streptomyces R61 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pwg | ||||||
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Title | Covalent Penicilloyl Acyl Enzyme Complex Of The Streptomyces R61 DD-Peptidase With A Highly Specific Penicillin | ||||||
Components | D-alanyl-D-alanine carboxypeptidase | ||||||
Keywords | HYDROLASE/ANTIBIOTIC / BETA-LACTAM / PENICILLIN BINDING PROTEIN / ENZYME / PEPTIDOGLYCAN / HYDROLASE-ANTIBIOTIC complex | ||||||
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: 1.074 Å | ||||||
Authors | Silvaggi, N.R. / Josephine, H.R. / Pratt, R.F. / Kelly, J.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 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: 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. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 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: Journal: J.Mol.Biol. / Year: 1995 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 HEL The ligand HEL in this structure is in its acylated form. The acylation ...ACYL FORM OF LIGAND HEL The ligand HEL in this structure is in its acylated form. The acylation reaction resulted in the removal of the covalent bond between atoms N4 and C7 of HEL 400, and the formation of the covalent bond between atom OG of SER 62 and atom C7 of HEL 400. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pwg.cif.gz | 170.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pwg.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pwg_validation.pdf.gz | 735.8 KB | Display | wwPDB validaton report |
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Full document | 1pwg_full_validation.pdf.gz | 738.2 KB | Display | |
Data in XML | 1pwg_validation.xml.gz | 20.2 KB | Display | |
Data in CIF | 1pwg_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pwg ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pwg | HTTPS FTP |
-Related structure data
Related structure data | 1pw1C 1pw8C 1pwcC 1pwdC 3pteS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 37422.574 Da / Num. of mol.: 1 / Fragment: DD-PEPTIDASE / 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-HE0 / ( |
#3: 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: 1.95 Å3/Da / Density % sol: 45.88 % |
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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: X12C / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: BRANDEIS - B4 / Detector: CCD / Date: Oct 27, 2002 / 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: 1.074→50 Å / Num. all: 147076 / Num. obs: 141081 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.074→1.12 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 9.9 / Num. unique all: 10531 / % possible all: 72.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3PTE Resolution: 1.074→10 Å / Num. parameters: 29613 / Num. restraintsaints: 36663 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.021.
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Refine analyze | Luzzati coordinate error obs: 0.06 Å / Num. disordered residues: 22 / Occupancy sum hydrogen: 542 / Occupancy sum non hydrogen: 3156.03 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.074→10 Å
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Refine LS restraints |
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