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Yorodumi- PDB-6alx: Structure of F. tularensis MglA-SspA solved in the presence of polyP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6alx | ||||||
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Title | Structure of F. tularensis MglA-SspA solved in the presence of polyP | ||||||
Components |
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Keywords | TRANSCRIPTION / MglA / SspA / Francisella tularensis / bioweapon / ppGpp | ||||||
Function / homology | Function and homology information Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle ...Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å | ||||||
Authors | Schumacher, M.A. | ||||||
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 | 6alx.cif.gz | 325.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6alx.ent.gz | 265.4 KB | Display | PDB format |
PDBx/mmJSON format | 6alx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/6alx ftp://data.pdbj.org/pub/pdb/validation_reports/al/6alx | HTTPS FTP |
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-Related structure data
Related structure data | 5u51C 5u56SC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24110.094 Da / Num. of mol.: 2 / Fragment: UNP residues 3-209 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: AV531_02990, DR86_1150 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZL39 #2: Protein | Mass: 23594.529 Da / Num. of mol.: 2 / Fragment: UNP residues 1-201 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: DR86_1530 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E2ZLH6 |
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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: 2.93 Å3/Da / Density % sol: 57.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Peg 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→60.754 Å / Num. obs: 16079 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Redundancy: 3.5 % / CC1/2: 0.994 / Rpim(I) all: 0.062 / Rrim(I) all: 0.117 / Rsym value: 0.098 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.5 / CC1/2: 0.843 / Rpim(I) all: 0.28 / Rrim(I) all: 0.643 / Rsym value: 0.448 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5U56 Resolution: 3.3→60.753 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.8
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Bsol: 62.129 Å2 / ksol: 0.309 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 350.4 Å2 / Biso mean: 96.9676 Å2 / Biso min: 20.46 Å2
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Refinement step | Cycle: final / Resolution: 3.3→60.753 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Origin x: 1.1972 Å / Origin y: 0.0225 Å / Origin z: 10.4491 Å
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Refinement TLS group |
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