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Yorodumi- PDB-8aif: TapA acts as specific chaperone in TasA non-amyloid filament formation -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aif | ||||||
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Title | TapA acts as specific chaperone in TasA non-amyloid filament formation | ||||||
Components | YqxM protein required for localization of TasA to extracellular matrix | ||||||
Keywords | STRUCTURAL PROTEIN / Bacillus subtilis / Biofilm / TasA / TapA/YqxM | ||||||
Function / homology | bacterial biofilm matrix / TasA anchoring/assembly protein / Signal peptide, camelysin / NITRATE ION / YqxM protein required for localization of TasA to extracellular matrix Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.07 Å | ||||||
Authors | Roske, Y. / Heinemann, U. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: TapA acts as specific chaperone in TasA filament formation by strand complementation. Authors: Roske, Y. / Lindemann, F. / Diehl, A. / Cremer, N. / Higman, V.A. / Schlegel, B. / Leidert, M. / Driller, K. / Turgay, K. / Schmieder, P. / Heinemann, U. / Oschkinat, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aif.cif.gz | 196.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aif.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 8aif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aif_validation.pdf.gz | 460.4 KB | Display | wwPDB validaton report |
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Full document | 8aif_full_validation.pdf.gz | 463.4 KB | Display | |
Data in XML | 8aif_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 8aif_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/8aif ftp://data.pdbj.org/pub/pdb/validation_reports/ai/8aif | HTTPS FTP |
-Related structure data
Related structure data | 6hqcSC 6qayC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 13779.772 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_0967 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164X7F2 #2: Chemical | ChemComp-NO3 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
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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: 2.11 Å3/Da / Density % sol: 41.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24% PEG3350, 0.35M LiNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→38.44 Å / Num. obs: 153127 / % possible obs: 98.8 % / Redundancy: 3.53 % / CC1/2: 0.999 / Rrim(I) all: 0.066 / Net I/σ(I): 9.77 |
Reflection shell | Resolution: 1.07→1.13 Å / Num. unique obs: 24261 / CC1/2: 0.3 / Rrim(I) all: 0.154 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HQC Resolution: 1.07→38.44 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.003 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 100.49 Å2 / Biso mean: 18.961 Å2 / Biso min: 8.59 Å2
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Refinement step | Cycle: final / Resolution: 1.07→38.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1735 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.07→1.097 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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