+Open data
-Basic information
Entry | Database: PDB / ID: 6z6s | ||||||||||||
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Title | Crystal structure of Uba4-Urm1 from Chaetomium thermophilum | ||||||||||||
Components |
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Keywords | TRANSFERASE / Ubiquitin-like protein activator 4 | ||||||||||||
Function / homology | Function and homology information molybdopterin synthase sulfurtransferase / molybdopterin-synthase sulfurtransferase activity / molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / tRNA thio-modification / tRNA wobble position uridine thiolation / ubiquitin-like modifier activating enzyme activity / protein urmylation / tRNA wobble uridine modification / Mo-molybdopterin cofactor biosynthetic process ...molybdopterin synthase sulfurtransferase / molybdopterin-synthase sulfurtransferase activity / molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / tRNA thio-modification / tRNA wobble position uridine thiolation / ubiquitin-like modifier activating enzyme activity / protein urmylation / tRNA wobble uridine modification / Mo-molybdopterin cofactor biosynthetic process / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.153 Å | ||||||||||||
Authors | Grudnik, P. / Pabis, M. / Ethiraju Ravichandran, K. / Glatt, S. | ||||||||||||
Funding support | Poland, 3items
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Citation | Journal: Embo J. / Year: 2020 Title: Molecular basis for the bifunctional Uba4-Urm1 sulfur-relay system in tRNA thiolation and ubiquitin-like conjugation. Authors: Pabis, M. / Termathe, M. / Ravichandran, K.E. / Kienast, S.D. / Krutyholowa, R. / Sokolowski, M. / Jankowska, U. / Grudnik, P. / Leidel, S.A. / Glatt, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z6s.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z6s.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/6z6s ftp://data.pdbj.org/pub/pdb/validation_reports/z6/6z6s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32247.521 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Gene: uba4, cnxF, CTHT_0055980 / Production host: Escherichia coli (E. coli) References: UniProt: G0SC54, molybdopterin-synthase adenylyltransferase, molybdopterin synthase sulfurtransferase |
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#2: Protein | Mass: 11421.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Gene: URM1, CTHT_0062030 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SE11 |
#3: Chemical | ChemComp-ZN / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.49 Å3/Da / Density % sol: 72.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Hepes pH 7.5 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 30, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→42.87 Å / Num. obs: 13003 / % possible obs: 99.78 % / Redundancy: 9.9 % / Biso Wilson estimate: 166.81 Å2 / CC1/2: 1 / CC star: 1 / Rrim(I) all: 0.066 / Rsym value: 0.06226 / Net I/σ(I): 18.85 |
Reflection shell | Resolution: 3.15→3.26 Å / Rmerge(I) obs: 5.447 / Num. unique obs: 1279 / CC1/2: 0.297 / CC star: 0.664 / Rpim(I) all: 1.91 / Rrim(I) all: 4.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: D_1292108208 Resolution: 3.153→42.87 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.924 / SU B: 28.309 / SU ML: 0.452 / Cross valid method: FREE R-VALUE / ESU R Free: 0.503 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 142.709 Å2
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Refinement step | Cycle: LAST / Resolution: 3.153→42.87 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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