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Yorodumi- PDB-3nb6: Crystal structure of Aquifex aeolicus peptidoglycan glycosyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nb6 | ||||||
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Title | Crystal structure of Aquifex aeolicus peptidoglycan glycosyltransferase in complex with Methylphosphoryl Neryl Moenomycin | ||||||
Components | Penicillin-binding protein 1A | ||||||
Keywords | TRANSFERASE / Glycosyltransferases / Peptidoglycan Glycosyltransferase / Polysaccharides / cell wall / antibiotics / moenomycin | ||||||
Function / homology | Function and homology information peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sliz, P. / Yuan, Y. / Walker, S. / Kahne, D. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2010 Title: Functional and structural analysis of a key region of the cell wall inhibitor moenomycin. Authors: Fuse, S. / Tsukamoto, H. / Yuan, Y. / Wang, T.S. / Zhang, Y. / Bolla, M. / Walker, S. / Sliz, P. / Kahne, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nb6.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nb6.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 3nb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/3nb6 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/3nb6 | HTTPS FTP |
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-Related structure data
Related structure data | 3nb7C 2oqoS 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: Protein | Mass: 22884.375 Da / Num. of mol.: 1 / Fragment: UNP residues 59-243 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: vf5 / Gene: aq_624, mrcA, ponA / Plasmid: PET48(B)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3) References: UniProt: O66874, Transferases; Glycosyltransferases; Pentosyltransferases |
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Nonpolymer details | METHYLPHOS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 MM HEPES, 6% PEG6K, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.7→28.52 Å / Num. obs: 7845 / % possible obs: 97.4 % / Biso Wilson estimate: 0 Å2 / Rsym value: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2oqo Resolution: 2.7→28.52 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 60732.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED. METHYLPHOSPHORYL NERYL MOENOMYCIN IS NOT MODELED IN THE COMPLEX STRUCTURE BECAUSE OF LOW OCCUPANCY BUT ELECTRON DENSITY MAP SHOWS CLEAR DENSITY OF LIGAND, ESPECIALLY ...Details: BULK SOLVENT MODEL USED. METHYLPHOSPHORYL NERYL MOENOMYCIN IS NOT MODELED IN THE COMPLEX STRUCTURE BECAUSE OF LOW OCCUPANCY BUT ELECTRON DENSITY MAP SHOWS CLEAR DENSITY OF LIGAND, ESPECIALLY THE PHOSPHATE ATOM IN THE LIGAND BINDING SITE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.5847 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→28.52 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 6
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Xplor file |
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