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Open data
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Basic information
Entry | Database: PDB / ID: 7zlw | ||||||
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Title | NME1 in complex with ADP | ||||||
![]() | Nucleoside diphosphate kinase A | ||||||
![]() | TRANSFERASE / NME1 / complex / nucleoside diphosphate kinase 1 / ADP | ||||||
Function / homology | ![]() intermediate filament binding / negative regulation of myeloid leukocyte differentiation / Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / mammary gland development / nucleoside-diphosphate kinase / gamma-tubulin binding / UTP biosynthetic process ...intermediate filament binding / negative regulation of myeloid leukocyte differentiation / Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / mammary gland development / nucleoside-diphosphate kinase / gamma-tubulin binding / UTP biosynthetic process / CTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / dTMP biosynthetic process / ribosomal small subunit binding / 3'-5' exonuclease activity / lactation / positive regulation of epithelial cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / ruffle membrane / positive regulation of neuron projection development / endocytosis / myelin sheath / nervous system development / single-stranded DNA binding / mitochondrial outer membrane / early endosome / cell differentiation / negative regulation of gene expression / centrosome / GTP binding / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / magnesium ion binding / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Garcia-Saez, I. / Iuso, D. / Khochbin, S. / Petosa, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet. Authors: Iuso, D. / Garcia-Saez, I. / Coute, Y. / Yamaryo-Botte, Y. / Boeri Erba, E. / Adrait, A. / Zeaiter, N. / Tokarska-Schlattner, M. / Jilkova, Z.M. / Boussouar, F. / Barral, S. / Signor, L. / ...Authors: Iuso, D. / Garcia-Saez, I. / Coute, Y. / Yamaryo-Botte, Y. / Boeri Erba, E. / Adrait, A. / Zeaiter, N. / Tokarska-Schlattner, M. / Jilkova, Z.M. / Boussouar, F. / Barral, S. / Signor, L. / Couturier, K. / Hajmirza, A. / Chuffart, F. / Bourova-Flin, E. / Vitte, A.L. / Bargier, L. / Puthier, D. / Decaens, T. / Rousseaux, S. / Botte, C. / Schlattner, U. / Petosa, C. / Khochbin, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 385.3 KB | Display | ![]() |
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PDB format | ![]() | 312.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7zl8C ![]() 7ztkC ![]() 2hvdS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17561.199 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: The chain E of hexameric NME1 does not have ADP bound. Some residues around the nucleotide binding region are disordered. Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P15532, nucleoside-diphosphate kinase #2: Chemical | ChemComp-ADP / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.05 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 400, NaCl, Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→59.65 Å / Num. obs: 40517 / % possible obs: 98.2 % / Redundancy: 2.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.028 / Rrim(I) all: 0.039 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3536 / CC1/2: 0.877 / Rpim(I) all: 0.309 / Rrim(I) all: 0.437 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2hvd Resolution: 2.2→59.65 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.5 / Stereochemistry target values: ML
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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 max: 107.21 Å2 / Biso mean: 38.0417 Å2 / Biso min: 10.55 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→59.65 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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