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Yorodumi- PDB-6scx: Crystal structure of the catalytic domain of human NUDT12 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6scx | ||||||
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Title | Crystal structure of the catalytic domain of human NUDT12 in complex with 7-methyl-guanosine-5'-triphosphate | ||||||
Components | Peroxisomal NADH pyrophosphatase NUDT12 | ||||||
Keywords | HYDROLASE / NUDIX protein / DENADDING enzyme | ||||||
Function / homology | Function and homology information NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / mRNA methylguanosine-cap decapping / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / NAD-cap decapping / NAD catabolic process / NAD biosynthesis via nicotinamide riboside salvage pathway ...NADP catabolic process / NAD+ diphosphatase / NAD+ diphosphatase activity / NADH pyrophosphatase activity / mRNA methylguanosine-cap decapping / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / NAD-cap decapping / NAD catabolic process / NAD biosynthesis via nicotinamide riboside salvage pathway / Nicotinamide salvaging / NADH metabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peroxisomal matrix / circadian regulation of gene expression / peroxisome / magnesium ion binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å | ||||||
Authors | McCarthy, A.A. / Chen, K.M. / Wu, H. / Li, L. / Homolka, D. / Gos, P. / Fleury-Olela, F. / Pillai, R.S. | ||||||
Citation | Journal: Cell Rep / Year: 2019 Title: Decapping Enzyme NUDT12 Partners with BLMH for Cytoplasmic Surveillance of NAD-Capped RNAs. Authors: Wu, H. / Li, L. / Chen, K.M. / Homolka, D. / Gos, P. / Fleury-Olela, F. / McCarthy, A.A. / Pillai, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6scx.cif.gz | 312.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6scx.ent.gz | 242.4 KB | Display | PDB format |
PDBx/mmJSON format | 6scx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/6scx ftp://data.pdbj.org/pub/pdb/validation_reports/sc/6scx | HTTPS FTP |
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-Related structure data
Related structure data | 6o3pS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/716 / Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/716 |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40000.852 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT12 / Plasmid: pETM-11-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BQG2, NAD+ diphosphatase #2: Chemical | ChemComp-CD / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.53 Å3/Da / Density % sol: 65.19 % / Description: Long rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.3 Details: 20% (w/v) PEG 3350 0.2M potassium citrate tribasic monohydrate 0.02M CdCl(2) 0.02M m7GTP |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.0077 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 27, 2019 / Details: Toroidal mirror |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0077 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→114.93 Å / Num. obs: 21142 / % possible obs: 95.8 % / Redundancy: 10.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.039 / Rrim(I) all: 0.124 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.9→3.2 Å / Redundancy: 9.4 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1057 / CC1/2: 0.633 / Rpim(I) all: 0.51 / Rrim(I) all: 1.56 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6O3P Resolution: 2.92→114.93 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.863 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.525
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Displacement parameters | Biso max: 258.63 Å2 / Biso mean: 94.16 Å2 / Biso min: 28.34 Å2
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Refine analyze | Luzzati coordinate error obs: 0.55 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.92→114.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.92→3.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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Refinement TLS params. | L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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