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Yorodumi- PDB-2wae: PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMON... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wae | ||||||
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Title | PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204) | ||||||
Components | PENICILLIN-BINDING PROTEIN 2B | ||||||
Keywords | PEPTIDE BINDING PROTEIN / PEPTIDOGLYCAN SYNTHESIS / PENICILLIN-BINDING PROTEIN / TRANSMEMBRANE / ANTIBIOTIC RESISTANCE / CELL SHAPE / PEPTIDOGLYCAN / CELL MEMBRANE / CELL WALL BIOGENESIS/DEGRADATION / MEMBRANE / INFECTION / RESISTANCE / ANTIBIOTIC | ||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | STREPTOCOCCUS PNEUMONIAE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Contreras-Martel, C. / Dahout-Gonzalez, C. / Dos-Santos-Martins, A. / Kotnik, M. / Dessen, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Pbp Active Site Flexibility as the Key Mechanism for Beta-Lactam Resistance in Pneumococci Authors: Contreras-Martel, C. / Dahout-Gonzalez, C. / Dos-Santos-Martins, A. / Kotnik, M. / Dessen, A. #1: Journal: Antimicrobial Agents and Che / Year: 2004 Title: Biochemical Characterization of Streptococcus Pneumoniae Penicillin-Binding Protein 2B and its Implication in Beta-Lactam Resistance Authors: Pagliero, E. / Chesnel, L. / Hopkins, J. / Croize, J. / Dideberg, O. / Vernet, T. / Di-Guilmi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wae.cif.gz | 134 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wae.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wae_validation.pdf.gz | 432.4 KB | Display | wwPDB validaton report |
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Full document | 2wae_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 2wae_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 2wae_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/2wae ftp://data.pdbj.org/pub/pdb/validation_reports/wa/2wae | HTTPS FTP |
-Related structure data
Related structure data | 2wadSC 2wafC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 73828.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: 5204 References: UniProt: P0A3M6, UniProt: B0B6I9*PLUS, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Sequence details | PBP2B STRAIN R6 P0A3M6 PROTEIN SEQUENCE CODE IS THE CLOSER ONE TO MUTANT STRAIN 5204 (58 MUTATIONS). ...PBP2B STRAIN R6 P0A3M6 PROTEIN SEQUENCE CODE IS THE CLOSER ONE TO MUTANT STRAIN 5204 (58 MUTATIONS). THE PROTEIN SEQUENCE OF PBP2B STRAIN 5204 WAS OBTAINED BY OUR COLLABORAT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % / Description: NONE |
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Crystal grow | pH: 8 Details: 100 MM BIS-TRIS-HCL PH 5.5, 300 MM NACL, 5 MM ZN ACETATE, 30% W/V POLYETHYLENE GLYCOL MME 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 8, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→54.39 Å / Num. obs: 38102 / % possible obs: 91.2 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 44.19 Å2 / Rsym value: 0.06 / Net I/σ(I): 21.69 |
Reflection shell | Resolution: 2.26→2.4 Å / Redundancy: 4 % / Mean I/σ(I) obs: 6.8 / Rsym value: 0.25 / % possible all: 82 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WAD Resolution: 2.26→54.39 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.891 / SU B: 24.267 / SU ML: 0.239 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.U VALUES RESIDUAL ONLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.26→54.39 Å
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