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Yorodumi- PDB-6b8c: Crystal structure of NlpC/p60 domain of peptidoglycan hydrolase SagA -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b8c | ||||||
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Title | Crystal structure of NlpC/p60 domain of peptidoglycan hydrolase SagA | ||||||
Components | NLP/P60 | ||||||
Keywords | HYDROLASE / peptidoglycan endopeptidase | ||||||
Function / homology | : Function and homology information | ||||||
Biological species | Enterococcus faecium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å | ||||||
Authors | Kim, B. / Oren, D.A. / Hang, H.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2019 Title: Enterococcus faeciumsecreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis. Authors: Kim, B. / Wang, Y.C. / Hespen, C.W. / Espinosa, J. / Salje, J. / Rangan, K.J. / Oren, D.A. / Kang, J.Y. / Pedicord, V.A. / Hang, H.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b8c.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b8c.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 6b8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/6b8c ftp://data.pdbj.org/pub/pdb/validation_reports/b8/6b8c | HTTPS FTP |
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-Related structure data
Related structure data | 4fdyS 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15715.212 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: FM130_01170 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A1T4J4N4 |
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#2: 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: 2.69 Å3/Da / Density % sol: 54.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 2 M ammonium sulfate, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 8107 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / CC1/2: 0.997 / Rpim(I) all: 0.035 / Rsym value: 0.109 / Χ2: 1.79 / Net I/σ(I): 38.5 |
Reflection shell | Χ2: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FDY Resolution: 2.403→44.894 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.38 / 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: 2.403→44.894 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 108.8705 Å / Origin y: 79.4809 Å / Origin z: 140.5608 Å
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Refinement TLS group | Selection details: all |