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Yorodumi- PDB-4ii9: Crystal structure of Weissella viridescens FemXVv non-ribosomal a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ii9 | |||||||||
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Title | Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate | |||||||||
Components |
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Keywords | TRANSFERASE/PEPTIDE/RNA / FEMX / PEPTIDOGLYCAN / transferase / peptidyl-RNA conjugate complex / TRANSFERASE-PEPTIDE-RNA 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) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | |||||||||
Authors | Li de la Sierra-Gallay, I. / Fonvielle, M. / van Tilbeurgh, H. / Arthur, M. / Etheve-Quelquejeu, M. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2013 Title: The Structure of FemXWv in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA(Ala) to Peptidoglycan Precursors Authors: Fonvielle, M. / Li de La Sierra-Gallay, I. / El-Sagheer, A.H. / Lecerf, M. / Patin, D. / Mellal, D. / Mayer, C. / Blanot, D. / Gale, N. / Brown, T. / van Tilbeurgh, H. / Etheve-Quelquejeu, M. / Arthur, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ii9.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ii9.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ii9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ii9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4ii9_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4ii9_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 4ii9_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ii/4ii9 ftp://data.pdbj.org/pub/pdb/validation_reports/ii/4ii9 | HTTPS FTP |
-Related structure data
Related structure data | 3gkrS S: Starting model for refinement |
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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
-Protein / Protein/peptide / RNA chain / 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) / Strain: CIP102810T / Gene: femX / Plasmid: pTrc-His60 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 References: UniProt: Q9EY50, UDP-N-acetylmuramoylpentapeptide-lysine N6-alanyltransferase |
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#2: Protein/peptide | Mass: 463.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide |
#3: RNA chain | Mass: 973.715 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide |
#6: Sugar | ChemComp-MUB / |
-Non-polymers , 3 types, 298 molecules
#4: Chemical | ChemComp-GOL / |
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#5: Chemical | ChemComp-UDP / |
#7: 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: 2.38 Å3/Da / Density % sol: 48.4 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M Tris-sodium citrate buffer, 0.2M ammonium acetate, 33% polyethylene glycol 4k, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2012 / Details: mirrors |
Radiation | Monochromator: channel cut cryogenically cooled monochromator crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→38.12 Å / Num. all: 44718 / Num. obs: 44718 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.66→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 6.9 / Num. unique all: 7126 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GKR Resolution: 1.66→38.12 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.632 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.328 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→38.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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