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Yorodumi- PDB-7z5z: CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z5z | |||||||||
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Title | CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE | |||||||||
Components |
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Keywords | TRANSFERASE / FEMX / Xeno-nucleic acids / PEPTIDOGLYCAN / PEPTIDYL-XNA CONJUGATE / TRANSFERASE-PEPTIDE-XNA COMPLEX | |||||||||
Function / homology | Function and homology information UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase / UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape Similarity search - Function | |||||||||
Biological species | Weissella viridescens (bacteria) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | |||||||||
Authors | Li de la Sierra-Gallay, I. | |||||||||
Funding support | France, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis. Authors: Rietmeyer, L. / Li De La Sierra-Gallay, I. / Schepers, G. / Dorchene, D. / Iannazzo, L. / Patin, D. / Touze, T. / van Tilbeurgh, H. / Herdewijn, P. / Etheve-Quelquejeu, M. / Fonvielle, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z5z.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z5z.ent.gz | 67.8 KB | Display | PDB format |
PDBx/mmJSON format | 7z5z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z5z_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7z5z_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7z5z_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 7z5z_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/7z5z ftp://data.pdbj.org/pub/pdb/validation_reports/z5/7z5z | HTTPS FTP |
-Related structure data
Related structure data | 7z5yC 7z6aC 7z6kC 4ii9S C: citing same article (ref.) 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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1 |
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Unit cell |
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-Components
-Protein / DNA chain / Protein/peptide / Sugars , 4 types, 4 molecules ABC
#1: Protein | Mass: 39212.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Weissella viridescens (bacteria) / Gene: femX / Production host: Escherichia coli (E. coli) References: UniProt: Q9EY50, UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase |
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#2: DNA chain | Mass: 1254.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein/peptide | Mass: 463.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#6: Sugar | ChemComp-MUB / |
-Non-polymers , 3 types, 274 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-UDP / |
#7: Water | ChemComp-HOH / |
-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: 2.39 Å3/Da / Density % sol: 48.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 5.6 / Details: Tri-Na citrate, Ammonium Acetate, PEG400 |
-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: 0.980107 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980107 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→45.16 Å / Num. obs: 60734 / % possible obs: 98.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.1 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.079 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.49→1.58 Å / Num. unique obs: 9291 / CC1/2: 0.53 / Rrim(I) all: 2.22 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4II9 Resolution: 1.49→45.16 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.31 / 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: 85.45 Å2 / Biso mean: 31.0993 Å2 / Biso min: 19.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→45.16 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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