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- PDB-3tg9: The crystal structure of penicillin binding protein from Bacillus... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tg9 | ||||||
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Title | The crystal structure of penicillin binding protein from Bacillus halodurans | ||||||
![]() | Penicillin-binding protein | ||||||
![]() | penicillin binding protein / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC | ||||||
Function / homology | Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta / Penicillin-binding protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Z. / Satyanarayana, L. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. ...Zhang, Z. / Satyanarayana, L. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
![]() | ![]() Title: The crystal structure of penicillin binding protein from Bacillus halodurans Authors: Zhang, Z. / Satyanarayana, L. / Almo, S.C. / Swaminathan, 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 | ![]() | 143.7 KB | Display | ![]() |
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PDB format | ![]() | 111.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.5 KB | Display | ![]() |
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Full document | ![]() | 447.2 KB | Display | |
Data in XML | ![]() | 27 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qmiS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40384.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350, 0.8% 1,4- butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 38211 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5.5 / Num. unique all: 3781 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2QMI Resolution: 2.2→49.999 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.19 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.334 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→49.999 Å
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Refine LS restraints |
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LS refinement shell |
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