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Yorodumi- PDB-5u56: Structure of Francisella tularensis heterodimeric SspA (MglA-SspA) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u56 | ||||||
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Title | Structure of Francisella tularensis heterodimeric SspA (MglA-SspA) | ||||||
Components |
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Keywords | TRANSCRIPTION / Stringent starvation protein A / Macrophage growth locus A / GST-fold | ||||||
Function / homology | Function and homology information Stringent starvation protein A, C-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like ...Stringent starvation protein A, C-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Francisella tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Cuthbert, B.J. / Schumacher, M.A. / Brennan, R.G. | ||||||
Citation | Journal: Genes Dev. / Year: 2017 Title: Dissection of the molecular circuitry controlling virulence in Francisella tularensis. Authors: Cuthbert, B.J. / Ross, W. / Rohlfing, A.E. / Dove, S.L. / Gourse, R.L. / Brennan, R.G. / Schumacher, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u56.cif.gz | 171.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u56.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 5u56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/5u56 ftp://data.pdbj.org/pub/pdb/validation_reports/u5/5u56 | HTTPS FTP |
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-Related structure data
Related structure data | 5u51C 6alxC 1yy7S 4purS 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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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules CDAB
#1: Protein | Mass: 24110.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: DR86_1150 / Plasmid: pMCSG21 / Details (production host): For coexpression / Cell line (production host): C41 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZL39, UniProt: Q5NHJ6*PLUS #2: Protein | Mass: 23594.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: DR86_1530 / Plasmid: pET28A Details (production host): Expressed as an MBP fusion protein from pMCSG9 Cell line (production host): C41 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZLH6, UniProt: Q5NFG1*PLUS |
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-Non-polymers , 4 types, 76 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | #6: 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: 2.77 Å3/Da / Density % sol: 55.55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEGRX2 17 L-proline, HEPES, PEG 1500 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 31478 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 31.74 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 2.13 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4PUR, 1YY7 Resolution: 2.65→44.077 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.32 / 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: 2.65→44.077 Å
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Refine LS restraints |
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LS refinement shell |
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