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Yorodumi- PDB-7qau: Crystal structure of a cyclodipeptide synthase from Parcubacteria... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qau | ||||||
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Title | Crystal structure of a cyclodipeptide synthase from Parcubacteria bacterium RAAC4_OD1_1, D58N mutant | ||||||
Components | Cyclodipeptide synthase | ||||||
Keywords | LIGASE / Cyclodipeptide synthase | ||||||
Function / homology | Cyclodipeptide synthase superfamily / Cyclodipeptide synthase / Cyclodipeptide synthase / aminoacyltransferase activity / Cyclodipeptide synthase Function and homology information | ||||||
Biological species | Parcubacteria bacterium RAAC4_OD1_1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Sutherland, E. / Harding, C.J. / Czekster, C.M. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Commun Chem / Year: 2022 Title: Active site remodelling of a cyclodipeptide synthase redefines substrate scope. Authors: Sutherland, E. / Harding, C.J. / Czekster, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qau.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qau.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 7qau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qau_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
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Full document | 7qau_full_validation.pdf.gz | 425.4 KB | Display | |
Data in XML | 7qau_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 7qau_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/7qau ftp://data.pdbj.org/pub/pdb/validation_reports/qa/7qau | HTTPS FTP |
-Related structure data
Related structure data | 7qaqC 7qatC 7qawC 7qaxC 7qayC 7qb8C 7qae S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28162.416 Da / Num. of mol.: 1 / Mutation: D58N Source method: isolated from a genetically manipulated source Details: C-terminal His Tag (EHHHHHH) Source: (gene. exp.) Parcubacteria bacterium RAAC4_OD1_1 (bacteria) Gene: O210_OD1C00001G0241 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V7PYQ5 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2.27 M Ammonium Sulfate 0.1 M Sodium Acetate pH 5.17 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→46.26 Å / Num. obs: 12429 / % possible obs: 99.3 % / Redundancy: 25.1 % / CC1/2: 1 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.018 / Rrim(I) all: 0.089 / Net I/σ(I): 27 / Num. measured all: 311398 / Scaling rejects: 196 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7QAE 7qae Resolution: 2.3→46.26 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.96 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 151.91 Å2 / Biso mean: 69.7855 Å2 / Biso min: 39.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→46.26 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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