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Yorodumi- PDB-6vhv: Klebsiella oxytoca NpsA in complex with 3-hydroxyanthranilyl-AMSN -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vhv | ||||||
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Title | Klebsiella oxytoca NpsA in complex with 3-hydroxyanthranilyl-AMSN | ||||||
Components | NpsA Adenylation Domain | ||||||
Keywords | BIOSYNTHETIC PROTEIN / adenylation / tilivalline / tilimycin / NRPS / nonribosomal peptide synthetase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Klebsiella oxytoca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Kreitler, D.F. / Gulick, A.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2020 Title: Biosynthesis, Mechanism of Action, and Inhibition of the Enterotoxin Tilimycin Produced by the Opportunistic PathogenKlebsiella oxytoca. Authors: Alexander, E.M. / Kreitler, D.F. / Guidolin, V. / Hurben, A.K. / Drake, E. / Villalta, P.W. / Balbo, S. / Gulick, A.M. / Aldrich, C.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vhv.cif.gz | 197.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vhv.ent.gz | 140.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vhv_validation.pdf.gz | 348.8 KB | Display | wwPDB validaton report |
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Full document | 6vhv_full_validation.pdf.gz | 349.6 KB | Display | |
Data in XML | 6vhv_validation.xml.gz | 1.5 KB | Display | |
Data in CIF | 6vhv_validation.cif.gz | 6.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/6vhv ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vhv | HTTPS FTP |
-Related structure data
Related structure data | 6vhtC 6vhuSC 6vhwC 6vhxC 6vhyC 6vhzC 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
#1: Protein | Mass: 55554.848 Da / Num. of mol.: 1 / Mutation: E312A, E313A, Q314A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Strain: NPSA / Gene: AGF18_11095 / Plasmid: pET15 / Details (production host): N-term TEV tag / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U4DY99 |
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#2: Chemical | ChemComp-QXG / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 296 K / Method: microbatch / pH: 6.6 Details: well solution: 400 mM imidazole pH 6.6, 10% w/v PEG8000/10000/12000/20000, 2.5% w/v 1,3-dimethylimidazolium dimethyl phosphate protein solution (16 mg/mL): 10 mM HEPES pH 8.0, 25 mM NaCl, 0. ...Details: well solution: 400 mM imidazole pH 6.6, 10% w/v PEG8000/10000/12000/20000, 2.5% w/v 1,3-dimethylimidazolium dimethyl phosphate protein solution (16 mg/mL): 10 mM HEPES pH 8.0, 25 mM NaCl, 0.4 mM TCEP, 5 mM 3HA-AMSN droplet: 2 uL protein solution, 1 uL well solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→68.1 Å / Num. obs: 12516 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 86.74 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Rsym value: 0.149 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.89→2.95 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 605 / CC1/2: 0.412 / Rpim(I) all: 0.858 / Rrim(I) all: 2.261 / Rsym value: 2.088 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6vhu Resolution: 2.89→68.1 Å / SU ML: 0.508 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.174
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 97.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→68.1 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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