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Yorodumi- PDB-6y4b: Structure of cyclodipeptide synthase from Candidatus Glomeribacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y4b | ||||||
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Title | Structure of cyclodipeptide synthase from Candidatus Glomeribacter gigasporarum bound to Phe-tRNAPhe | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / cyclodipeptide synthase / tRNA / Complex | ||||||
Function / homology | PHENYLALANINE / RNA / RNA (> 10) / Uncharacterized protein Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) Candidatus Glomeribacter gigasporarum BEG34 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5 Å | ||||||
Authors | Bourgeois, G. / Mechulam, Y. / Schmitt, E. | ||||||
Funding support | France, 1items
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Citation | Journal: Rna / Year: 2020 Title: Structural basis of the interaction between cyclodipeptide synthases and aminoacylated tRNA substrates. Authors: Bourgeois, G. / Seguin, J. / Babin, M. / Gondry, M. / Mechulam, Y. / Schmitt, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y4b.cif.gz | 207.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y4b.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 6y4b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y4/6y4b ftp://data.pdbj.org/pub/pdb/validation_reports/y4/6y4b | HTTPS FTP |
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-Related structure data
Related structure data | 6y3gC 5mlpS 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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Unit cell |
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-Components
#1: RNA chain | Mass: 24519.662 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: tRNA is aminoacylated, adenosine 76 is bounded to phenylalanine Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 34119.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Glomeribacter gigasporarum BEG34 (bacteria) Gene: CAGGBEG34_30028 / Production host: Escherichia coli (E. coli) / References: UniProt: G2JBB2 |
#3: Chemical | ChemComp-PHE / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.55 Å3/Da / Density % sol: 77.84 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 10% PEG8000, 0.17 M AcCa, 0.17 M Guanidinium hydrochloride, 0.1 M Hepes pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 5→50 Å / Num. obs: 6120 / % possible obs: 95.6 % / Redundancy: 33.2 % / Biso Wilson estimate: 214.56 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 5→5.3 Å / Redundancy: 32 % / Mean I/σ(I) obs: 1 / Num. unique obs: 867 / CC1/2: 0.58 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MLP Resolution: 5→48.16 Å / SU ML: 1.0625 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.2752 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 139.07 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 5→48.16 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -80.2336000483 Å / Origin y: 69.1408391067 Å / Origin z: 3.14746588878 Å
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Refinement TLS group | Selection details: all |