+Open data
-Basic information
Entry | Database: PDB / ID: 2j7v | ||||||
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Title | Structure of PBP-A | ||||||
Components | TLL2115 PROTEIN | ||||||
Keywords | HYDROLASE / PENICILLIN-BINDING PROTEIN / LACTAMASE / DD-PEPTIDASE / THIOESTERASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 2j7v.cif.gz | 427.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j7v.ent.gz | 354.7 KB | Display | PDB format |
PDBx/mmJSON format | 2j7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j7v_validation.pdf.gz | 458 KB | Display | wwPDB validaton report |
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Full document | 2j7v_full_validation.pdf.gz | 471.1 KB | Display | |
Data in XML | 2j7v_validation.xml.gz | 48.3 KB | Display | |
Data in CIF | 2j7v_validation.cif.gz | 71.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/2j7v ftp://data.pdbj.org/pub/pdb/validation_reports/j7/2j7v | HTTPS FTP |
-Related structure data
Related structure data | 2j8yC 2j9oC 2jbfC 1bsgS 1e25S 1ermS 1i2sS 1mf0S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 32804.316 Da / Num. of mol.: 4 / Fragment: RESIDUES 93-368 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: Water | ChemComp-HOH / | 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 | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP. PROTEIN 10 MG/ML. RESERVOIR 500 UL HEPES 0.1 M PH 7.5, PROLINE 0.2 M, PEG-3350 10% (W/V) AND NAN3 0.02% (W/V). DROP 1UL PROTEIN AND 1 UL RESERVOIR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8414 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 2, 2004 Details: MIRROR 1, FLAT PRE-MIRROR. MIRROR 2, BENT, VERTICALLY FOCUSSING |
Radiation | Monochromator: SI , HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8414 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.2 Å / Num. obs: 94191 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.8 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PRE-ALIGNED STRUCTURES WITH PDB ENTRIES 1MF0, 1E25, 1BSG, 1ERM, 1I2S Resolution: 1.9→39.2 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.475 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.132 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.09 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→39.2 Å
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Refine LS restraints |
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