+Open data
-Basic information
Entry | Database: PDB / ID: 7f8m | ||||||||||||
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Title | Roadblock from Thorarchaeota SMTZ1-45 | ||||||||||||
Components | Robl_LC7 domain-containing protein | ||||||||||||
Keywords | UNKNOWN FUNCTION / Asgard archaea / MGLB / roadblock | ||||||||||||
Function / homology | Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Robl_LC7 domain-containing protein Function and homology information | ||||||||||||
Biological species | Candidatus Thorarchaeota archaeon SMTZ1-45 (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.14 Å | ||||||||||||
Authors | Robinson, R.C. / Tran, L.T. | ||||||||||||
Funding support | Japan, United States, 3items
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Citation | Journal: To Be Published Title: Roadblock from Thorarchaeota SMTZ1-45 Authors: Tran, L.T. / Robinson, R.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f8m.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f8m.ent.gz | 116.6 KB | Display | PDB format |
PDBx/mmJSON format | 7f8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f8m_validation.pdf.gz | 439.3 KB | Display | wwPDB validaton report |
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Full document | 7f8m_full_validation.pdf.gz | 452 KB | Display | |
Data in XML | 7f8m_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 7f8m_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/7f8m ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f8m | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 12750.568 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Thorarchaeota archaeon SMTZ1-45 (archaea) Gene: AM325_09185 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A135VIJ8 #2: 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: 2.55 Å3/Da / Density % sol: 51.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 100 mM CH3COONa pH 5.0, 200 mM LiCl 16% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→20 Å / Num. obs: 40561 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.043 / Rsym value: 0.095 / Net I/σ(I): 35.2 |
Reflection shell | Resolution: 2.14→2.19 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3449 / CC1/2: 0.664 / Rpim(I) all: 0.332 / Rrim(I) all: 0.689 / % possible all: 98 |
-Processing
Software |
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Refinement | Resolution: 2.14→20 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Displacement parameters | Biso mean: 37.96 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.14→2.22 Å
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