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Yorodumi- PDB-3d3h: Crystal structure of a complex of the peptidoglycan glycosyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d3h | ||||||
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Title | Crystal structure of a complex of the peptidoglycan glycosyltransferase domain from Aquifex aeolicus and neryl moenomycin A | ||||||
Components | Penicillin-insensitive transglycosylase | ||||||
Keywords | TRANSFERASE/ANTIBIOTIC / peptidoglycan glycosyltransferase / cell wall biosynthesis / antibiotics / penicillin-binding protein / transglycosylase / moenomycin / Antibiotic resistance / Cell shape / Cell wall biogenesis/degradation / Hydrolase / Inner membrane / Membrane / Multifunctional enzyme / Peptidoglycan synthesis / Signal-anchor / Transmembrane / TRANSFERASE-ANTIBIOTIC COMPLEX | ||||||
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: 2.31 Å | ||||||
Authors | Yuan, Y. / Sliz, P. / Walker, S. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2008 Title: Structural analysis of the contacts anchoring moenomycin to peptidoglycan glycosyltransferases and implications for antibiotic design. Authors: Yuan, Y. / Fuse, S. / Ostash, B. / Sliz, P. / Kahne, D. / Walker, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d3h.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d3h.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 3d3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/3d3h ftp://data.pdbj.org/pub/pdb/validation_reports/d3/3d3h | HTTPS FTP |
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-Related structure data
Related structure data | 2oqoS 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
#1: Protein | Mass: 22912.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: 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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#2: Chemical | ChemComp-M4O / ( |
#3: 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: 3.13 Å3/Da / Density % sol: 60.72 % |
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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 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2007 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.31→50 Å / Num. obs: 12059 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.059 |
Reflection shell | Resolution: 2.31→2.39 Å / Rsym value: 0.396 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2OQO Resolution: 2.31→28.59 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 102724.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.9162 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.31→28.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.31→2.45 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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