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Yorodumi- PDB-8es6: Crystal structure of an unusual amidase ClbL from colibactin gene... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8es6 | ||||||
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Title | Crystal structure of an unusual amidase ClbL from colibactin gene cluster | ||||||
Components | Colibactin biosynthesis amidase ClbL | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Amidase / Colibactin / Cancer | ||||||
Function / homology | Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Colibactin biosynthesis amidase ClbL Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tripathi, P. / Bruner, S.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Structural basis of the amidase ClbL central to the biosynthesis of the genotoxin colibactin. Authors: Tripathi, P. / Mousa, J.J. / Guntaka, N.S. / Bruner, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8es6.cif.gz | 183 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8es6.ent.gz | 143.6 KB | Display | PDB format |
PDBx/mmJSON format | 8es6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8es6_validation.pdf.gz | 442.7 KB | Display | wwPDB validaton report |
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Full document | 8es6_full_validation.pdf.gz | 454.5 KB | Display | |
Data in XML | 8es6_validation.xml.gz | 33.8 KB | Display | |
Data in CIF | 8es6_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/8es6 ftp://data.pdbj.org/pub/pdb/validation_reports/es/8es6 | HTTPS FTP |
-Related structure data
Related structure data | 5h6sS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53784.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: clbL, C1Q91_005015, D3C88_26935, E3O05_09855, E4T84_20070, ELT23_23620, ELT33_24240, ELT38_03815, ELY31_20800, EWK56_23785, FPI65_12350, H0O51_25470, HMW38_10405, IFB95_001929 Production host: Escherichia coli (E. coli) / References: UniProt: Q0P7K2 #2: Water | ChemComp-HOH / | 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: 1.98 Å3/Da / Density % sol: 37.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8.5, 30% PEG3500 |
-Data collection
Diffraction | Mean temperature: 277 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.55 Å / Num. obs: 66681 / % possible obs: 99.88 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1258 / Net I/σ(I): 10.74 |
Reflection shell | Resolution: 1.9→1.96 Å / Num. unique obs: 6614 / CC1/2: 0.73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5H6S Resolution: 1.9→49.55 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.04 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 90.11 Å2 / Biso mean: 34.6048 Å2 / Biso min: 12.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→49.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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