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- PDB-2ynt: GIM-1-3Mol native. Crystal structures of Pseudomonas aeruginosa G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ynt | ||||||
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Title | GIM-1-3Mol native. Crystal structures of Pseudomonas aeruginosa GIM- 1: active site plasticity in metallo-beta-lactamases | ||||||
![]() | (GIM-1 PROTEIN) x 2 | ||||||
![]() | HYDROLASE / ANTIBIOTIC RESISTANCE / RESIDUE DETERMINANTS / LOOP DYNAMICS | ||||||
Function / homology | ![]() antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Borra, P.S. / Samuelsen, O. / Spencer, J. / Lorentzen, M.S. / Leiros, H.-K.S. | ||||||
![]() | ![]() Title: Crystal Structures of Pseudomonas Aeruginosa Gim-1: Active-Site Plasticity in Metallo-Beta-Lactamases. Authors: Borra, P.S. / Samuelsen, O. / Spencer, J. / Walsh, T.R. / Lorentzen, M.S. / Leiros, H.-K.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 | ![]() | 163.3 KB | Display | ![]() |
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PDB format | ![]() | 127.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457 KB | Display | ![]() |
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Full document | ![]() | 460.1 KB | Display | |
Data in XML | ![]() | 33.2 KB | Display | |
Data in CIF | ![]() | 50.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ynuC ![]() 2ynvC ![]() 2ynwC ![]() 1ddkS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25619.758 Da / Num. of mol.: 2 / Fragment: RESIDUES 19-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | | Mass: 25633.785 Da / Num. of mol.: 1 / Fragment: RESIDUES 19-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | RESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED. A ...RESIDUES 1-18 IN THE GENE SEQUENCE ARE REMOVED AND A HIS TAG AND TEV CLEAVE SITE WAS INTRODUCED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.97 % / Description: NONE |
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Crystal grow | Details: 0.1M TRIS PH 7.1, 21% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000 (PEG MME 2K), 4% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.24 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 84988 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 14.48 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 0 |
Reflection shell | Resolution: 1.6→1.68 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 0 / % possible all: 90.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1DDK Resolution: 1.598→19.987 Å / SU ML: 0.14 / σ(F): 0.24 / Phase error: 18.45 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.598→19.987 Å
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Refine LS restraints |
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LS refinement shell |
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