[English] 日本語
Yorodumi- PDB-6rxj: Crystal structure of CobB wt in complex with H4K16-Acetyl peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rxj | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of CobB wt in complex with H4K16-Acetyl peptide | |||||||||
Components |
| |||||||||
Keywords | HYDROLASE / deacylase / NAD-dependent / Acetyl / Lysine / PTM | |||||||||
Function / homology | Function and homology information lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication ...lipoamidase activity / NAD-dependent protein de-2-hydroxyisobutyrylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / cyclic-di-GMP binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / replication fork protection complex / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / positive regulation of transcription by RNA polymerase I / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / NAD+-protein poly-ADP-ribosyltransferase activity / NAD+ binding / structural constituent of chromatin / chemotaxis / nucleosome / nucleosome assembly / chromatin organization / defense response to virus / protein heterodimerization activity / regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / zinc ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å | |||||||||
Authors | Spinck, M. / Gasper, R. / Neumann, H. | |||||||||
Funding support | Germany, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6rxj.cif.gz | 196.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6rxj.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 6rxj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rxj_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6rxj_full_validation.pdf.gz | 452.4 KB | Display | |
Data in XML | 6rxj_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 6rxj_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/6rxj ftp://data.pdbj.org/pub/pdb/validation_reports/rx/6rxj | HTTPS FTP |
-Related structure data
Related structure data | 6rxkC 6rxlC 6rxmC 6rxoC 6rxpC 6rxqC 6rxrC 6rxsC 1s5pS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
2 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 40 - 274 / Label seq-ID: 15 - 249
|
-Components
#1: Protein | Mass: 28106.750 Da / Num. of mol.: 2 / Fragment: H4K16Ac 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 #2: Protein/peptide | Mass: 1197.457 Da / Num. of mol.: 2 / Source method: obtained synthetically Source: (synth.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) References: UniProt: P02309 #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.53 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Bis-Tris, 0.03 M HCl, 22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→46.379 Å / Num. obs: 66812 / % possible obs: 99.9 % / Redundancy: 13.001 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.07 / Χ2: 1.02 / Net I/σ(I): 18.83 / Num. measured all: 868617 / Scaling rejects: 22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S5P Resolution: 1.6→46.379 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.76 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.93 Å2 / Biso mean: 39.1659 Å2 / Biso min: 17.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→46.379 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
|