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Yorodumi- PDB-6a02: Salmonella Typhi YfdX in the F222 space group at 1.4 A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 6a02 | ||||||
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Title | Salmonella Typhi YfdX in the F222 space group at 1.4 A resolution | ||||||
Components | YfdX protein | ||||||
Keywords | UNKNOWN FUNCTION / STY3178 / YfdX / Salmonella | ||||||
Function / homology | Function and homology information YfdX protein domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2140 / Uncharacterised protein family YfdX / YfdX protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology | ||||||
Biological species | Salmonella enterica I (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Ku, B. / Lee, H.S. / Kim, S.J. | ||||||
Citation | Journal: Front Microbiol / Year: 2018 Title: Structural and Physiological Exploration ofSalmonellaTyphi YfdX Uncovers Its Dual Function in Bacterial Antibiotic Stress and Virulence. Authors: Lee, H.S. / Lee, S. / Kim, J.S. / Lee, H.R. / Shin, H.C. / Lee, M.S. / Jin, K.S. / Kim, C.H. / Ku, B. / Ryu, C.M. / Kim, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6a02.cif.gz | 54.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6a02.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 6a02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6a02_validation.pdf.gz | 423.7 KB | Display | wwPDB validaton report |
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Full document | 6a02_full_validation.pdf.gz | 423.6 KB | Display | |
Data in XML | 6a02_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 6a02_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/6a02 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/6a02 | HTTPS FTP |
-Related structure data
Related structure data | 6a07C 6a09C 3dzaS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20630.119 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica I (bacteria) / Gene: yfdX, CVR97_27555, SE14_03224 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7DJF1, UniProt: A0A0D6IF67*PLUS | ||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #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: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M sodium acetate (pH 4.6), 2.5 M sodium chloride, 12% PEG1500, 1.5% 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 38242 / % possible obs: 98.8 % / Redundancy: 9.4 % / Rpim(I) all: 0.029 / Net I/σ(I): 41.3 |
Reflection shell | Resolution: 1.4→1.42 Å / Num. unique obs: 1853 / Rpim(I) all: 0.113 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DZA Resolution: 1.4→27.045 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.79 / Phase error: 19.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→27.045 Å
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Refine LS restraints |
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LS refinement shell |
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