+Open data
-Basic information
Entry | Database: PDB / ID: 6v3z | ||||||
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Title | Structure of Salmonella enteritidis Sen1395 | ||||||
Components | Sen1395 | ||||||
Keywords | PROTEIN TRANSPORT / Muramidase Lysozyme-like Peptidoglycan-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Salmonella enteritidis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Galan, J.E. / Lara-Tejero, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Elife / Year: 2020 Title: Mechanisms of substrate recognition by a typhoid toxin secretion-associated muramidase. Authors: Geiger, T. / Lara-Tejero, M. / Xiong, Y. / Galan, J.E. #1: Journal: To Be Published Title: Mechanisms of substrate recognition by a typhoid toxin secretion-associated muramidase Authors: Geiger, T. / Lara-Tejero, M. / Xiong, Y. / Galan, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6v3z.cif.gz | 154.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6v3z.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 6v3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6v3z_validation.pdf.gz | 433.3 KB | Display | wwPDB validaton report |
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Full document | 6v3z_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 6v3z_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 6v3z_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v3/6v3z ftp://data.pdbj.org/pub/pdb/validation_reports/v3/6v3z | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 11 - 186 / Label seq-ID: 21 - 196
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-Components
#1: Protein | Mass: 22457.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enteritidis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1R2HMX1 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate pH 7.0 and 20% w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→49.27 Å / Num. obs: 26682 / % possible obs: 89.85 % / Redundancy: 2.6 % / CC1/2: 0.98 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.25 |
Reflection shell | Resolution: 1.904→1.972 Å / Rmerge(I) obs: 0.572 / Num. unique obs: 2484 / CC1/2: 0.376 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TTSA Resolution: 1.9→49.27 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 12.728 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.678 Å2
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Refinement step | Cycle: final / Resolution: 1.9→49.27 Å
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Refine LS restraints |
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