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Yorodumi- PDB-1pw1: Non-Covalent Complex Of Streptomyces R61 DD-Peptidase With A High... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pw1 | ||||||
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Title | Non-Covalent Complex Of Streptomyces R61 DD-Peptidase With A Highly Specific Penicillin | ||||||
Components | D-alanyl-D-alanine carboxypeptidaseMuramoylpentapeptide carboxypeptidase | ||||||
Keywords | HYDROLASE / BETA-LACTAM / ANTIBIOTICS / PENICILLIN BINDING PROTEIN / ENZYME / PEPTIDOGLYCAN | ||||||
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: 1.2 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 | MISSING LIGAND ATOMS Atom O for ligand FOR missing due to loss-of-water reaction with CE1 of ...MISSING LIGAND ATOMS Atom O for ligand FOR missing due to loss-of-water reaction with CE1 of TYR159, NZ of LYS65, and NE2 of HIS108, resulting in covalent bond formation from C FOR600 to CE1 TYR159 and NZ LYS65, and from C FOR601 to NE2 HIS108 and NZ LYS65 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pw1.cif.gz | 168.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pw1.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pw1 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pw1 | HTTPS FTP |
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-Related structure data
Related structure data | 1pw8C 1pwcC 1pwdC 1pwgC 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-HEL / ( | ||||
#3: Chemical | #4: Chemical | #5: 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: 1.96 Å3/Da / Density % sol: 46.49 % |
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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 298K |
-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 |
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Reflection | Resolution: 1.2→20 Å / Num. all: 104613 / Num. obs: 104613 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 40.4 | |||||||||
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 6.2 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3PTE Resolution: 1.2→10 Å / Num. parameters: 28578 / Num. restraintsaints: 34599 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.039.
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Refine analyze | Luzzati coordinate error obs: 0.06 Å / Num. disordered residues: 22 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3056.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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