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Yorodumi- PDB-5tnj: Crystal structure of the E153Q mutant of the CFTR inhibitory fact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tnj | ||||||||||||||||||
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Title | Crystal structure of the E153Q mutant of the CFTR inhibitory factor Cif containing the adducted 4-Vinyl-1-cyclohexene 1,2-epoxide hydrolysis intermediate | ||||||||||||||||||
Components | CFTR inhibitory factor | ||||||||||||||||||
Keywords | HYDROLASE / epoxide hydrolase / hydroxyalkyl-enzyme intermediate | ||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||||||||||||||
Authors | Hvorecny, K.L. / Madden, D.R. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Structure / Year: 2017 Title: Active-Site Flexibility and Substrate Specificity in a Bacterial Virulence Factor: Crystallographic Snapshots of an Epoxide Hydrolase. Authors: Hvorecny, K.L. / Bahl, C.D. / Kitamura, S. / Lee, K.S.S. / Hammock, B.D. / Morisseau, C. / Madden, D.R. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tnj.cif.gz | 496.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tnj.ent.gz | 407.6 KB | Display | PDB format |
PDBx/mmJSON format | 5tnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tnj_validation.pdf.gz | 509.5 KB | Display | wwPDB validaton report |
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Full document | 5tnj_full_validation.pdf.gz | 517.3 KB | Display | |
Data in XML | 5tnj_validation.xml.gz | 54.2 KB | Display | |
Data in CIF | 5tnj_validation.cif.gz | 79.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tn/5tnj ftp://data.pdbj.org/pub/pdb/validation_reports/tn/5tnj | HTTPS FTP |
-Related structure data
Related structure data | 5tndC 5tneC 5tnfC 5tngC 5tnhC 5tniC 5tnkC 5tnlC 5tnmC 5tnnC 5tnpC 5tnqC 5tnrC 5tnsC 3kd2S S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34163.715 Da / Num. of mol.: 4 / Mutation: E153Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria) Strain: UCBPP-PA14 / Gene: PA14_26090 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: A0A0M3KL26, UniProt: A0A0H2ZD27*PLUS |
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-Non-polymers , 5 types, 1146 molecules
#2: Chemical | ChemComp-AVH / ( | ||||
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#3: Chemical | ChemComp-8MD / ( | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has protein modification | Y |
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Nonpolymer details | Ligand AVH ((1R,2R,4R)-4-ethenylcyclohexane-1,2-diol) or 8MD ((1S,2S,4S)-4-ethenylcyclohexane-1,2- ...Ligand AVH ((1R,2R,4R)-4-ethenylcyclohexane-1,2-diol) or 8MD ((1S,2S,4S)-4-ethenylcyclohexane-1,2-diol ) covalently linked to the protein Cif-E153Q, via its C1 atom to OD1 on Asp129 of the protein chain A; In chain B, C and D, ligand BVH ((1R,2R,4S)-4-ethenylcyclohexane-1,2-diol) or DVH ((1S,2S,4R)-4-ethenylcyclohexane-1,2-diol) covalently linked to the protein Cif-E153Q, via its C6 atom to OD1 on Asp129 of the protein. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: sodium acetate, pH5 calcium chloride PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→19.905 Å / Num. obs: 145788 / % possible obs: 99.8 % / Redundancy: 7.49 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Net I/σ(I): 28.02 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 6.99 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 6.08 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KD2 Resolution: 1.65→19.905 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.28 / 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: 1.65→19.905 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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