+Open data
-Basic information
Entry | Database: PDB / ID: 5x5r | ||||||
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Title | Crystal structure of a hydrolase from Listeria innocua | ||||||
Components | Lin2189 protein | ||||||
Keywords | HYDROLASE / crystal structure enzyme | ||||||
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 / Lin2189 protein Function and homology information | ||||||
Biological species | Listeria innocua serovar 6a | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.644 Å | ||||||
Authors | Zhang, J. / Zhou, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua Authors: Zhang, J. / Zhou, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x5r.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x5r.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 5x5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x5r_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
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Full document | 5x5r_full_validation.pdf.gz | 445.1 KB | Display | |
Data in XML | 5x5r_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 5x5r_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/5x5r ftp://data.pdbj.org/pub/pdb/validation_reports/x5/5x5r | HTTPS FTP |
-Related structure data
Related structure data | 3b49S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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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 Details: the density map of some residues Source: (gene. exp.) Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262) (bacteria) Strain: ATCC BAA-680 / CLIP 11262 / Gene: lin2189 / Production host: Escherichia coli (E. coli) / References: UniProt: Q929T5 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 34.75 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, glycerol, MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: CCD / Date: Jan 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 1.644→50 Å / Num. obs: 45205 / % possible obs: 98.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.5 |
Reflection shell | Rmerge(I) obs: 0.728 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3b49 Resolution: 1.644→29.395 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.49 / 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: 1.644→29.395 Å
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Refine LS restraints |
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LS refinement shell |
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