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- PDB-3zhh: X-ray structure of the full-length beta-lactamase from M.tuberculosis -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zhh | ||||||
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Title | X-ray structure of the full-length beta-lactamase from M.tuberculosis | ||||||
![]() | BETA-LACTAMASE | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() : / : / beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Feiler, C. / Fisher, A.C. / Marrichi, M.J. / Wright, L. / Schmidpeter, P.A.M. / Blankenfeldt, W. / Pavelka, M. / DeLisa, M.P. | ||||||
![]() | ![]() Title: Directed Evolution of Mycobacterium Tuberculosis Beta-Lactamase Reveals Gatekeeper Residue that Regulates Antibiotic Resistance and Catalytic Efficiency. Authors: Feiler, C. / Fisher, A.C. / Boock, J.T. / Marrichi, M.J. / Wright, L. / Schmidpeter, P.A.M. / Blankenfeldt, W. / Pavelka, M. / Delisa, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 368.8 KB | Display | ![]() |
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PDB format | ![]() | 305.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465 KB | Display | ![]() |
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Full document | ![]() | 473.4 KB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 52.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2gdnS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29296.867 Da / Num. of mol.: 4 / Fragment: RESIDUES 32-307 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0C5C1, UniProt: P9WKD3*PLUS, beta-lactamase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | pH: 7.8 / Details: 100MM TRIS PH 7.8 2.1 M (NH4)2SO4 (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→19.87 Å / Num. obs: 36698 / % possible obs: 99.7 % / Observed criterion σ(I): 4.07 / Redundancy: 3.2 % / Biso Wilson estimate: 33.26 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.52 |
Reflection shell | Resolution: 2.85→2.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.07 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2GDN Resolution: 2.85→19.872 Å / SU ML: 0.34 / σ(F): 2 / Phase error: 22.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→19.872 Å
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Refine LS restraints |
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LS refinement shell |
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