+Open data
-Basic information
Entry | Database: PDB / ID: 6z9l | ||||||||||||
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Title | Enterococcal PrgA | ||||||||||||
Components |
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Keywords | CELL ADHESION / Protease domain / CAP domain / coiled-coil | ||||||||||||
Function / homology | SEC10/PgrA surface exclusion domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / membrane / PrgA Function and homology information | ||||||||||||
Biological species | Enterococcus faecalis (bacteria) Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.063 Å | ||||||||||||
Authors | Berntsson, R.P.A. / Schmitt, A. | ||||||||||||
Funding support | Sweden, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: Enterococcal PrgA Extends Far Outside the Cell and Provides Surface Exclusion to Protect against Unwanted Conjugation. Authors: Schmitt, A. / Hirt, H. / Jarva, M.A. / Sun, W.S. / Ter Beek, J. / Dunny, G.M. / Berntsson, R.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z9l.cif.gz | 287 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z9l.ent.gz | 234.4 KB | Display | PDB format |
PDBx/mmJSON format | 6z9l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z9l_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 6z9l_full_validation.pdf.gz | 468.2 KB | Display | |
Data in XML | 6z9l_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 6z9l_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z9/6z9l ftp://data.pdbj.org/pub/pdb/validation_reports/z9/6z9l | HTTPS FTP |
-Related structure data
Related structure data | 6z9kSC 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: 87250.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: prgA / Production host: Escherichia coli (E. coli) / References: UniProt: Q04111 | ||||
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#2: Protein/peptide | Mass: 657.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #3: Chemical | ChemComp-SO4 / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.62 Å3/Da / Density % sol: 83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 37.5% (v/v) PEG400, 0.1 M Tris/HCl (pH 8.5), 0.114 M LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976247 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976247 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.06→49.107 Å / Num. obs: 45500 / % possible obs: 99.5 % / Redundancy: 12.682 % / Biso Wilson estimate: 102.72 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.255 / Rrim(I) all: 0.266 / Χ2: 1.076 / Net I/σ(I): 8.56 / Num. measured all: 577045 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Z9K Resolution: 3.063→49.107 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.8 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 598.68 Å2 / Biso mean: 134.9054 Å2 / Biso min: 32.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.063→49.107 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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