+Open data
-Basic information
Entry | Database: PDB / ID: 7jgt | ||||||
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Title | Crystal Structure of FN3tt | ||||||
Components | Fibronectin type-III domain-containing protein | ||||||
Keywords | STRUCTURAL PROTEIN / Hyperthermal stability / Surface Salt Bridges | ||||||
Function / homology | Function and homology information IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin E-set / Immunoglobulin-like fold Similarity search - Domain/homology | ||||||
Biological species | Caldanaerobacter subterraneus subsp. tengcongensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Model details | Crystal Structure of FN3tt, a Fibronectin-like Domain from T. tengcongensis | ||||||
Authors | Luo, J. / Malia, T.J. | ||||||
Citation | Journal: Proteins / Year: 2022 Title: Surface salt bridges contribute to the extreme thermal stability of an FN3-like domain from a thermophilic bacterium. Authors: Boucher, L. / Somani, S. / Negron, C. / Ma, W. / Jacobs, S. / Chan, W. / Malia, T. / Obmolova, G. / Teplyakov, A. / Gilliland, G.L. / Luo, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jgt.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jgt.ent.gz | 21.7 KB | Display | PDB format |
PDBx/mmJSON format | 7jgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jgt_validation.pdf.gz | 419.3 KB | Display | wwPDB validaton report |
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Full document | 7jgt_full_validation.pdf.gz | 420.1 KB | Display | |
Data in XML | 7jgt_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 7jgt_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/7jgt ftp://data.pdbj.org/pub/pdb/validation_reports/jg/7jgt | HTTPS FTP |
-Related 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: 11321.529 Da / Num. of mol.: 1 / Fragment: FN3-like Domain, residues 1458-1547 / Mutation: T68C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria) Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: TTE0165 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RD81 |
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#2: 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: 1.73 Å3/Da / Density % sol: 28.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M MES pH 6.5, 28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 18, 2007 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: OsmicTM VariMaxTM confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→31.11 Å / Num. obs: 6681 / % possible obs: 98.3 % / Redundancy: 24.13 % / Biso Wilson estimate: 27.131 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.065 / Χ2: 0.94 / Net I/σ(I): 38.63 / Num. measured all: 161213 / Scaling rejects: 4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Rosetta generated Resolution: 1.9→31.11 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.95 / 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: 62.19 Å2 / Biso mean: 22.8862 Å2 / Biso min: 9.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→31.11 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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