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Yorodumi- PDB-6rxs: Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rxs | |||||||||
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Title | Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl peptide | |||||||||
Components |
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Keywords | HYDROLASE / deacylase / NAD / NAD-dependent / Acetyl / Lysine | |||||||||
Function / homology | Function and homology information lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / cyclic-di-GMP binding / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / NAD+ ADP-ribosyltransferase activity / NAD+ binding ...lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / cyclic-di-GMP binding / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / NAD+ ADP-ribosyltransferase activity / NAD+ binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / chemotaxis / nucleosome / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / defense response to virus / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / Amyloid fiber formation / protein heterodimerization activity / protein homodimerization activity / protein-containing complex / DNA binding / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.599 Å | |||||||||
Authors | Spinck, M. / Gasper, R. / Neumann, H. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Evolved, Selective Erasers of Distinct Lysine Acylations. Authors: Spinck, M. / Neumann-Staubitz, P. / Ecke, M. / Gasper, R. / Neumann, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rxs.cif.gz | 106.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rxs.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/6rxs ftp://data.pdbj.org/pub/pdb/validation_reports/rx/6rxs | HTTPS FTP |
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-Related structure data
Related structure data | 6rxjC 6rxkC 6rxlC 6rxmC 6rxoC 6rxpC 6rxqC 6rxrC 1s5pS S: Starting model for refinement C: citing same article (ref.) |
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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: 28064.670 Da / Num. of mol.: 1 / Mutation: A76G,Y92A, I131L, V187Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: cobB, ycfY, b1120, JW1106 / Plasmid: pBAD / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P75960, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides | ||||
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#2: Protein/peptide | Mass: 1310.615 Da / Num. of mol.: 1 / Fragment: H4K16Ac / Mutation: K16ALY / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62805 | ||||
#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97792876162 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97792876162 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→42.165 Å / Num. obs: 34254 / % possible obs: 98.9 % / Redundancy: 6.49 % / Biso Wilson estimate: 14.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rrim(I) all: 0.11 / Χ2: 0.918 / Net I/σ(I): 17.56 / Num. measured all: 222321 / Scaling rejects: 506 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdbid 1S5P Resolution: 1.599→42.165 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.24 / 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: 108.52 Å2 / Biso mean: 26.3026 Å2 / Biso min: 7.08 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.599→42.165 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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