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Yorodumi- PDB-1pwd: Covalent acyl enzyme complex of the Streptomyces R61 DD-peptidase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pwd | ||||||
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Title | Covalent acyl enzyme complex of the Streptomyces R61 DD-peptidase with cephalosporin C | ||||||
Components | D-alanyl-D-alanine carboxypeptidase precursor | ||||||
Keywords | HYDROLASE/Antibiotic / BETA-LACTAM / ANTIBIOTICS / PENICILLIN BINDING PROTEIN / ENZYME / PEPTIDOGLYCAN / HYDROLASE / 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: 1.2 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pwd.cif.gz | 165.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pwd.ent.gz | 127.4 KB | Display | PDB format |
PDBx/mmJSON format | 1pwd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pwd_validation.pdf.gz | 814.6 KB | Display | wwPDB validaton report |
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Full document | 1pwd_full_validation.pdf.gz | 818.1 KB | Display | |
Data in XML | 1pwd_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 1pwd_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/1pwd ftp://data.pdbj.org/pub/pdb/validation_reports/pw/1pwd | HTTPS FTP |
-Related structure data
Related structure data | 1pw1C 1pw8C 1pwcC 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-0MU / ( |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE LIGAND 0MU REPRESENTS THE BOUND FORM OF THE ANTIBIOTIC CEPHALOSPORIN C. THE ACYLATION REACTION ...THE LIGAND 0MU REPRESENTS |
-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: 46.12 % |
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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: Apr 15, 2003 / 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→60 Å / Num. all: 102353 / Num. obs: 102353 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1 | |||||||||
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4 / Num. unique all: 7443 / % possible all: 70 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3PTE Resolution: 1.2→10 Å / Num. parameters: 28084 / Num. restraintsaints: 33924 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.024.
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Refine analyze | Luzzati coordinate error obs: 0.08 Å / Num. disordered residues: 11 / Occupancy sum hydrogen: 261 / Occupancy sum non hydrogen: 3061.9 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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