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Yorodumi- PDB-2ynt: GIM-1-3Mol native. Crystal structures of Pseudomonas aeruginosa G... -
+Open data
-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 | ||||||
Components | (GIM-1 PROTEIN) x 2 | ||||||
Keywords | HYDROLASE / ANTIBIOTIC RESISTANCE / RESIDUE DETERMINANTS / LOOP DYNAMICS | ||||||
Function / homology | Function and homology information antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å | ||||||
Authors | Borra, P.S. / Samuelsen, O. / Spencer, J. / Lorentzen, M.S. / Leiros, H.-K.S. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ynt.cif.gz | 163.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ynt.ent.gz | 127.8 KB | Display | PDB format |
PDBx/mmJSON format | 2ynt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/2ynt ftp://data.pdbj.org/pub/pdb/validation_reports/yn/2ynt | HTTPS FTP |
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-Related structure data
Related structure data | 2ynuC 2ynvC 2ynwC 1ddkS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS PRARE / References: UniProt: Q704V1 #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.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS PRARE / References: UniProt: Q704V1 #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: X-RAY DIFFRACTION |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.24 |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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