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Yorodumi- PDB-3mzf: Structure of penicillin-binding protein 5 from E. coli: imipenem ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mzf | ||||||
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Title | Structure of penicillin-binding protein 5 from E. coli: imipenem acyl-enzyme complex | ||||||
Components | D-alanyl-D-alanine carboxypeptidase dacA | ||||||
Keywords | HYDROLASE/ANTIBIOTIC / BETA-LACTAM ANTIBIOTIC / PENICILLIN-BINDING PROTEIN / DD-CARBOXYPEPTIDASE / HYDROLASE / HYDROLASE-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape ...peptidoglycan metabolic process / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / carboxypeptidase activity / cell wall organization / beta-lactamase activity / beta-lactamase / regulation of cell shape / outer membrane-bounded periplasmic space / protein homodimerization activity / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Nicola, G. / Tomberg, J. / Pratt, R.F. / Nicholas, R.A. / Davies, C. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Crystal structures of covalent complexes of beta-lactam antibiotics with Escherichia coli penicillin-binding protein 5: toward an understanding of antibiotic specificity Authors: Nicola, G. / Tomberg, J. / Pratt, R.F. / Nicholas, R.A. / Davies, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mzf.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mzf.ent.gz | 131.7 KB | Display | PDB format |
PDBx/mmJSON format | 3mzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mzf_validation.pdf.gz | 712 KB | Display | wwPDB validaton report |
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Full document | 3mzf_full_validation.pdf.gz | 716 KB | Display | |
Data in XML | 3mzf_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 3mzf_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/3mzf ftp://data.pdbj.org/pub/pdb/validation_reports/mz/3mzf | HTTPS FTP |
-Related structure data
Related structure data | 3mzdC 3mzeC 1nzoS 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: 39841.117 Da / Num. of mol.: 1 / Fragment: Soluble construct Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0632, dacA, JW0627, pfv / Plasmid: PBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 References: UniProt: P0AEB2, serine-type D-Ala-D-Ala carboxypeptidase, beta-lactamase |
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#2: Chemical | ChemComp-IM2 / ( |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Sequence details | AUTHORS STATE THAT THIS IS A SOLUBLE CONSTRUCT OF PBP 5. THE FIRST 29 AMINO ACIDS OF THE PROTEIN, ...AUTHORS STATE THAT THIS IS A SOLUBLE CONSTRUCT OF PBP 5. THE FIRST 29 AMINO ACIDS OF THE PROTEIN, WHICH ENCODE THE SIGNAL SEQUENCE, ARE NOT INCLUDED. THE LAST 17 AMINO ACIDS OF THE WILD-TYPE SEQUENCE ARE ALSO ABSENT AND ARE REPLACED BY SIX NON-NATIVE AMINO ACIDS (GDPVID - INTRODUCED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 MM TRIS PH 7.0, 8 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 24, 2004 |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR SI-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33 Å / Num. all: 61886 / Num. obs: 61886 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 40.1 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4880 / Rsym value: 0.488 / % possible all: 76.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 1NZO Resolution: 1.5→32.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.01 / SU ML: 0.051 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→32.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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