+Open data
-Basic information
Entry | Database: PDB / ID: 8rzl | ||||||
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Title | Sulfolobus acidocaldarius threads (0406) filament. | ||||||
Components | Sulfolobus acidocaldarius threads (0406) filament. | ||||||
Keywords | PROTEIN FIBRIL / cell surface appendage / N-glycosylation / O-glycosylation | ||||||
Function / homology | alpha-D-mannopyranose / Uncharacterized protein Function and homology information | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.65 Å | ||||||
Authors | Isupov, M.N. / Gaines, M. / McLaren, M. / Daum, B. | ||||||
Funding support | European Union, 1items
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Citation | Journal: To Be Published Title: Sulfolobus acidocaldarius threads (0406) filament. Authors: Isupov, M.N. / Gaines, M. / McLaren, M. / Daum, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rzl.cif.gz | 226.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rzl.ent.gz | 193.1 KB | Display | PDB format |
PDBx/mmJSON format | 8rzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rzl_validation.pdf.gz | 3.2 MB | Display | wwPDB validaton report |
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Full document | 8rzl_full_validation.pdf.gz | 3.2 MB | Display | |
Data in XML | 8rzl_validation.xml.gz | 44.9 KB | Display | |
Data in CIF | 8rzl_validation.cif.gz | 62.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/8rzl ftp://data.pdbj.org/pub/pdb/validation_reports/rz/8rzl | HTTPS FTP |
-Related structure data
Related structure data | 19608MC M: map data used to model this data 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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-Components
#1: Protein | Mass: 19720.252 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Sulfolobus acidocaldarius (acidophilic) / References: UniProt: Q4JBK8 #2: Polysaccharide | beta-D-glucopyranose-(1-4)-6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)] ...beta-D-glucopyranose-(1-4)-6-deoxy-6-sulfo-beta-D-glucopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Type: oligosaccharide / Mass: 1137.028 Da / Num. of mol.: 25 Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-MAN / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Filament 0406 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Sulfolobus acidocaldarius (acidophilic) |
Buffer solution | pH: 3 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 2.57 sec. / Electron dose: 43.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 20579 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -103.281 ° / Axial rise/subunit: 31.65 Å / Axial symmetry: C1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 626078 / Symmetry type: HELICAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Resolution: 2.65→212.22 Å / Cor.coef. Fo:Fc: 0.936 / SU B: 4.785 / SU ML: 0.085 / ESU R: 0.089 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Solvent model: PARAMETERS FOR MASK CACLULATION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 106.998 Å2
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Refinement step | Cycle: 1 / Total: 8895 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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