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Yorodumi- PDB-6mkh: Crystal structure of pencillin binding protein 4 (PBP4) from Ente... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mkh | ||||||
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Title | Crystal structure of pencillin binding protein 4 (PBP4) from Enterococcus faecalis in the imipenem-bound form | ||||||
Components | pencillin binding protein 4 (PBP4) | ||||||
Keywords | protein binding/antibiotic / PBP / antibiotic / inhibitor / imipenem / PENICILLIN-BINDING PROTEIN / protein binding-antibiotic complex | ||||||
Function / homology | Function and homology information peptidoglycan L,D-transpeptidase activity / penicillin binding / cell wall organization / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Enterococcus faecalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | D'Andrea, E.D. / Moon, T.M. / Peti, W. / Page, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: The structures of penicillin-binding protein 4 (PBP4) and PBP5 fromEnterococciprovide structural insights into beta-lactam resistance. Authors: Moon, T.M. / D'Andrea, E.D. / Lee, C.W. / Soares, A. / Jakoncic, J. / Desbonnet, C. / Garcia-Solache, M. / Rice, L.B. / Page, R. / Peti, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mkh.cif.gz | 106.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mkh.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 6mkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mkh_validation.pdf.gz | 697.8 KB | Display | wwPDB validaton report |
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Full document | 6mkh_full_validation.pdf.gz | 702 KB | Display | |
Data in XML | 6mkh_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 6mkh_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mk/6mkh ftp://data.pdbj.org/pub/pdb/validation_reports/mk/6mkh | HTTPS FTP |
-Related structure data
Related structure data | 6bsqC 6bsrC 6mkaC 6mkfC 6mkgC 6mkiC 6mkjC 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: 70709.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: pbp4, A6B47_10405, DAI13_12160 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K3C9 | ||
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#2: Chemical | ChemComp-IM2 / ( | ||
#3: Chemical | #4: 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: 2.89 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 3.25 / Details: 0.04M KH2PO4, 16% PEG 8000, 20% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 12, 2017 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→37.895 Å / Num. obs: 77350 / % possible obs: 96 % / Redundancy: 4.6 % / Biso Wilson estimate: 48.35 Å2 / CC1/2: 0.959 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.047 / Rrim(I) all: 0.075 / Χ2: 0.72 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.62→2.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2364 / CC1/2: 0.321 / Rpim(I) all: 0.181 / Rrim(I) all: 0.28 / Χ2: 0.46 / % possible all: 77.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PBP4 apo Resolution: 2.62→37.895 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.38 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→37.895 Å
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Refine LS restraints |
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LS refinement shell |
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