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Yorodumi- PDB-6o6e: Crystal structure of PltF trapped with PltL using a proline adeno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o6e | ||||||||||||
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Title | Crystal structure of PltF trapped with PltL using a proline adenosine vinylsulfonamide inhibitor | ||||||||||||
Components |
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Keywords | Ligase/Transport protein / nonribosomal peptide synthetase / NRPS / type II / biosynthesis / pyoluteorin / Ligase-Transport protein complex | ||||||||||||
Function / homology | Function and homology information L-proline-[L-prolyl-carrier protein] ligase / peptide transport / ligase activity / antibiotic biosynthetic process / ATP binding Similarity search - Function | ||||||||||||
Biological species | Pseudomonas protegens Pf-5 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||||||||
Authors | Corpuz, J.C. / Podust, L.M. | ||||||||||||
Funding support | United States, 2items
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Citation | Journal: Rsc Chem Biol / Year: 2020 Title: Dynamic visualization of type II peptidyl carrier protein recognition in pyoluteorin biosynthesis. Authors: Corpuz, J.C. / Podust, L.M. / Davis, T.D. / Jaremko, M.J. / Burkart, M.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o6e.cif.gz | 134.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o6e.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 6o6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o6e_validation.pdf.gz | 762.8 KB | Display | wwPDB validaton report |
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Full document | 6o6e_full_validation.pdf.gz | 771.3 KB | Display | |
Data in XML | 6o6e_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 6o6e_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/6o6e ftp://data.pdbj.org/pub/pdb/validation_reports/o6/6o6e | HTTPS FTP |
-Related structure data
Related structure data | 3e7wS 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules BE
#1: Protein | Mass: 56397.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: pltF, PFL_2792 / Plasmid: pET37b / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q4KCY5, L-proline-[L-prolyl-carrier protein] ligase |
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#2: Protein | Mass: 11141.683 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: pltL, PFL_2786 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q4KCZ1 |
-Non-polymers , 5 types, 121 molecules
#3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-TRS / | #5: Chemical | #6: Chemical | ChemComp-I5M / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 4.09 Å3/Da / Density % sol: 69.93 % / Description: hexagonal prism, approximately 50 um long |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.73 / Details: 0.1 M malonic acid pH 5.73, 3.18 M sodium formate |
-Data collection
Diffraction | Mean temperature: 110 K / Ambient temp details: liquid nitrogen stream / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2018 / Details: mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→85.42 Å / Num. obs: 59600 / % possible obs: 99.2 % / Redundancy: 10.03 % / Biso Wilson estimate: 59.78 Å2 / CC1/2: 0.998 / CC star: 1 / Rrim(I) all: 0.2803 / Net I/σ(I): 9.73 |
Reflection shell | Resolution: 2.14→2.19 Å / Redundancy: 8.48 % / Mean I/σ(I) obs: 0.31 / Num. unique obs: 5360 / CC1/2: 0.0817 / CC star: 0.389 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3E7W Resolution: 2.14→85.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.97 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.68 Å2 / Biso mean: 58.52 Å2 / Biso min: 35.18 Å2
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Refinement step | Cycle: final / Resolution: 2.14→85.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.145→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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