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- PDB-2zc3: Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biape... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zc3 | ||||||
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Title | Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae | ||||||
![]() | (Penicillin-binding protein ...) x 3 | ||||||
![]() | BIOSYNTHETIC PROTEIN / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / PENICILLIN-BINDING / ANTIBIOTICS / BIAPENEM / Antibiotic resistance / Cell cycle / Cell division / Cell shape / Cell wall biogenesis/degradation / Membrane / Secreted / Transmembrane | ||||||
Function / homology | ![]() penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamada, M. / Watanabe, T. / Takeuchi, Y. | ||||||
![]() | ![]() Title: Crystal Structures of Biapenem and Tebipenem Complexed with Penicillin-Binding Proteins 2X and 1A from Streptococcus pneumoniae Authors: Yamada, M. / Watanabe, T. / Baba, N. / Takeuchi, Y. / Ohsawa, F. / Gomi, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.8 KB | Display | ![]() |
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PDB format | ![]() | 202.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 553.3 KB | Display | ![]() |
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Full document | ![]() | 559.5 KB | Display | |
Data in XML | ![]() | 25.2 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zc4C ![]() 2zc5C ![]() 2zc6C ![]() 2z2lS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Penicillin-binding protein ... , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 18473.584 Da / Num. of mol.: 2 / Fragment: UNP residues 71-238 Source method: isolated from a genetically manipulated source Details: N-terminal domain / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 42000.016 Da / Num. of mol.: 2 / Fragment: UNP residues 241-625 Source method: isolated from a genetically manipulated source Details: Transpeptidase domain / Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 13707.433 Da / Num. of mol.: 2 / Fragment: UNP residues 626-750 Source method: isolated from a genetically manipulated source Details: C-terminal domain / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 3 types, 85 molecules ![](data/chem/img/BMG.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10-25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 16, 2006 Details: A fixed exit SI double crystal monochromator followed bystandard double crystal monochromator and RH-coated downward-deflection mirror with a typical glancing angle of 3.7MRAD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.51 Å / Num. obs: 53714 / % possible obs: 92.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 52.76 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.5→2.58 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 5.5 / % possible all: 90.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Z2L Resolution: 2.5→29.51 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.417 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.594 / ESU R Free: 0.326 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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