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Yorodumi- PDB-2jbf: Structure of PBP-A, L158E mutant. Acyl-enzyme complex with penici... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jbf | ||||||
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Title | Structure of PBP-A, L158E mutant. Acyl-enzyme complex with penicillin- G. | ||||||
Components | TLL2115 PROTEIN | ||||||
Keywords | HYDROLASE / PENICILLIN-BINDING PROTEIN / LACTAMASE / THIOESTERASE / DD-PEPTIDASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / response to antibiotic Similarity search - Function | ||||||
Biological species | SYNECHOCOCCUS ELONGATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å | ||||||
Authors | Evrard, C. / Declercq, J.-P. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure of Pbp-A from Thermosynechococcus Elongatus, a Penicillin-Binding Protein Closely Related to Class a Beta-Lactamases. Authors: Urbach, C. / Evrard, C. / Pudzaitis, V. / Fastrez, J. / Soumillion, P. / Declercq, J.-P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jbf.cif.gz | 431.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jbf.ent.gz | 368.8 KB | Display | PDB format |
PDBx/mmJSON format | 2jbf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jbf ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jbf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 32820.270 Da / Num. of mol.: 4 / Fragment: RESIDUES 93-368 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: BP-1 / Description: CYANOBASE / Plasmid: PBAD-MYC-HIS-TETR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP 10 References: UniProt: Q8DH45, serine-type D-Ala-D-Ala carboxypeptidase #2: Chemical | ChemComp-PNM / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, LEU 249 TO GLU ENGINEERED RESIDUE IN CHAIN B, LEU 249 TO GLU ...ENGINEERED | Sequence details | CRYSTALLIN | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 46 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: SEE ENTRY 2J9O, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.843 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 2005 Details: MIRROR 1, FLAT PRE-MIRROR. MIRROR 2, BENT, VERTICALLY FOCUSSING |
Radiation | Monochromator: SI 111, HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.843 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28 Å / Num. obs: 126686 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.7→1.75 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.7→77.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.856 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→77.61 Å
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Refine LS restraints |
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