+Open data
-Basic information
Entry | Database: PDB / ID: 6zk7 | ||||||
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Title | Crystal Structure of human PYROXD1/FAD complex | ||||||
Components | Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1 | ||||||
Keywords | OXIDOREDUCTASE / redox regulation / NAD(P)(H) binding / tRNA ligase complex / flavoprotein | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor / sarcomere / cellular response to oxidative stress / oxidoreductase activity / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Meinhart, A. / Asanovic, I. / Martinez, J. / Clausen, T. | ||||||
Citation | Journal: Mol.Cell / Year: 2021 Title: The oxidoreductase PYROXD1 uses NAD(P) + as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response. Authors: Asanovic, I. / Strandback, E. / Kroupova, A. / Pasajlic, D. / Meinhart, A. / Tsung-Pin, P. / Djokovic, N. / Anrather, D. / Schuetz, T. / Suskiewicz, M.J. / Sillamaa, S. / Kocher, T. / ...Authors: Asanovic, I. / Strandback, E. / Kroupova, A. / Pasajlic, D. / Meinhart, A. / Tsung-Pin, P. / Djokovic, N. / Anrather, D. / Schuetz, T. / Suskiewicz, M.J. / Sillamaa, S. / Kocher, T. / Beveridge, R. / Nikolic, K. / Schleiffer, A. / Jinek, M. / Hartl, M. / Clausen, T. / Penninger, J. / Macheroux, P. / Weitzer, S. / Martinez, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zk7.cif.gz | 209.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zk7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zk7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zk7_validation.pdf.gz | 699.5 KB | Display | wwPDB validaton report |
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Full document | 6zk7_full_validation.pdf.gz | 700.8 KB | Display | |
Data in XML | 6zk7_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 6zk7_validation.cif.gz | 20.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/6zk7 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/6zk7 | HTTPS FTP |
-Related structure data
Related structure data | 4bv6S S: Starting model for refinement |
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Similar 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: 56977.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PYROXD1 / Production host: Escherichia coli (E. coli) References: UniProt: Q8WU10, Oxidoreductases; Acting on a sulfur group of donors; With NAD+ or NADP+ as acceptor |
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#2: Chemical | ChemComp-FAD / |
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: 3.77 Å3/Da / Density % sol: 67.38 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.7 Details: 2 M (NH4)2SO4 0.5 g/ml PEG 400 100 mM MES-NaOH pH 6.7 100 mM CH3COOLi 5 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Nov 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. obs: 26957 / % possible obs: 99.3 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rrim(I) all: 0.11 / Net I/σ(I): 13.58 |
Reflection shell | Resolution: 3.2→3.28 Å / Mean I/σ(I) obs: 1.24 / Num. unique obs: 1997 / CC1/2: 0.561 / Rrim(I) all: 1.864 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BV6 Resolution: 3.2→19.95 Å / SU ML: 0.3958 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.6783 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 123.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→19.95 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: AAAA / Label asym-ID: A
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