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Yorodumi- PDB-4mxe: Human ESCO1 (Eco1/Ctf7 ortholog), acetyltransferase domain in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mxe | ||||||
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Title | Human ESCO1 (Eco1/Ctf7 ortholog), acetyltransferase domain in complex with acetyl-CoA | ||||||
Components | N-acetyltransferase ESCO1 | ||||||
Keywords | TRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / GCN5-related N-acetyltransferase fold / ACETYLTRANSFERASE / NUCLEUS | ||||||
Function / homology | Function and homology information post-translational protein acetylation / Establishment of Sister Chromatid Cohesion / peptidyl-lysine acetylation / N-acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / mitotic sister chromatid cohesion / regulation of DNA replication / acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / chromosome ...post-translational protein acetylation / Establishment of Sister Chromatid Cohesion / peptidyl-lysine acetylation / N-acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / mitotic sister chromatid cohesion / regulation of DNA replication / acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / chromosome / chromatin / zinc ion binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Karlberg, T. / Wisniewska, M. / Thorsell, A.G. / Kouznetsova, E. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. ...Karlberg, T. / Wisniewska, M. / Thorsell, A.G. / Kouznetsova, E. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Kallas, A. / Kraulis, P. / Kotenyova, T. / Moche, M. / Nielsen, T.K. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Svensson, L. / Tresaugues, L. / Van Den Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Structure / Year: 2016 Title: Sister Chromatid Cohesion Establishment Factor ESCO1 Operates by Substrate-Assisted Catalysis. Authors: Kouznetsova, E. / Kanno, T. / Karlberg, T. / Thorsell, A.G. / Wisniewska, M. / Kursula, P. / Sjogren, C. / Schuler, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mxe.cif.gz | 155.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mxe.ent.gz | 131.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mxe_validation.pdf.gz | 1009.8 KB | Display | wwPDB validaton report |
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Full document | 4mxe_full_validation.pdf.gz | 1018.5 KB | Display | |
Data in XML | 4mxe_validation.xml.gz | 17 KB | Display | |
Data in CIF | 4mxe_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/4mxe ftp://data.pdbj.org/pub/pdb/validation_reports/mx/4mxe | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23998.846 Da / Num. of mol.: 2 / Fragment: Acetyltransferase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EFO1, ESCO1, KIAA1911 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold pRARE References: UniProt: Q5FWF5, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 49.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.4M dipotassium hydrogen phosphate, 1.6M sodium hydrogen phosphate and 0.1M phosphate citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 2, 2009 |
Radiation | Monochromator: Double Crystal Monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→35 Å / Num. all: 15312 / Num. obs: 15312 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.053 / Net I/σ(I): 28.1 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1107 / Rsym value: 0.338 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.6→33.17 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.894 / SU B: 21.266 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.753 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→33.17 Å
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