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- PDB-5x5m: Crystal structure of a hydrolase encoded by lin2189 from Listeria... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5x5m | ||||||
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Title | Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua | ||||||
![]() | Lin2189 protein | ||||||
![]() | HYDROLASE/ANTIBIOTIC / hydrolase / HYDROLASE-ANTIBIOTIC complex | ||||||
Function / homology | ![]() GyrI-like cyclopropanoid cyclopropyl hydrolase Lin2189-like / GyrI-like small molecule binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / GyrI-like small molecule binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Listeria innocua serovar 6a | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, J. | ||||||
![]() | ![]() Title: GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection Authors: Yuan, H. / Zhang, J. / Cai, Y. / Wu, S. / Yang, K. / Chan, H.C.S. / Huang, W. / Jin, W.B. / Li, Y. / Yin, Y. / Igarashi, Y. / Yuan, S. / Zhou, J. / Tang, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111.5 KB | Display | ![]() |
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PDB format | ![]() | 84.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 884.5 KB | Display | ![]() |
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Full document | ![]() | 895.6 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3b49S 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25363.141 Da / Num. of mol.: 2 / Mutation: E157A/E185L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-680 / CLIP 11262 / Gene: lin2189 / Production host: ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.01 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 4000, Glycerol, MES/imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97791 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→50 Å / Num. obs: 112031 / % possible obs: 96 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.025 / Net I/σ(I): 30.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3B49 Resolution: 1.211→44.039 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19 / 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: 1.211→44.039 Å
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Refine LS restraints |
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LS refinement shell |
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