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- PDB-4mxe: Human ESCO1 (Eco1/Ctf7 ortholog), acetyltransferase domain in com... -

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Basic information

Entry
Database: PDB / ID: 4mxe
TitleHuman ESCO1 (Eco1/Ctf7 ortholog), acetyltransferase domain in complex with acetyl-CoA
ComponentsN-acetyltransferase ESCO1
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC / GCN5-related N-acetyltransferase fold / ACETYLTRANSFERASE / NUCLEUS
Function / homology
Function and homology information


post-translational protein acetylation / peptidyl-lysine acetylation / Establishment of Sister Chromatid Cohesion / N-acetyltransferase activity / sister chromatid cohesion / protein-lysine-acetyltransferase activity / mitotic sister chromatid cohesion / acetyltransferase activity / regulation of DNA replication / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups ...post-translational protein acetylation / peptidyl-lysine acetylation / Establishment of Sister Chromatid Cohesion / N-acetyltransferase activity / sister chromatid cohesion / protein-lysine-acetyltransferase activity / mitotic sister chromatid cohesion / acetyltransferase activity / regulation of DNA replication / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / chromosome / chromatin / zinc ion binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
N-acetyltransferase ESCO, zinc-finger / N-acetyltransferase ESCO, acetyl-transferase domain / zinc-finger of acetyl-transferase ESCO / ESCO1/2 acetyl-transferase
Similarity search - Domain/homology
ACETYL COENZYME *A / N-acetyltransferase ESCO1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsKarlberg, 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)
CitationJournal: 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
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase ESCO1
B: N-acetyltransferase ESCO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6174
Polymers47,9982
Non-polymers1,6192
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-18 kcal/mol
Surface area19280 Å2
MethodPISA
2
A: N-acetyltransferase ESCO1
B: N-acetyltransferase ESCO1
hetero molecules

A: N-acetyltransferase ESCO1
B: N-acetyltransferase ESCO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2348
Polymers95,9954
Non-polymers3,2384
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area13790 Å2
ΔGint-65 kcal/mol
Surface area33620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.333, 66.333, 211.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein N-acetyltransferase ESCO1 / CTF7 homolog 1 / Establishment factor-like protein 1 / EFO1p / hEFO1 / Establishment of cohesion 1 ...CTF7 homolog 1 / Establishment factor-like protein 1 / EFO1p / hEFO1 / Establishment of cohesion 1 homolog 1 / ECO1 homolog 1 / ESO1 homolog 1


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 ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 2, 2009
RadiationMonochromator: Double Crystal Monochromator Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
MxCuBEdata collection
Auto-Rickshawphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.27943 1533 10 %RANDOM
Rwork0.22089 ---
all0.22672 13811 --
obs0.22672 13789 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.42 Å20 Å2-0 Å2
2---1.42 Å20 Å2
3---2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 102 20 2982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193024
X-RAY DIFFRACTIONr_bond_other_d0.0030.022894
X-RAY DIFFRACTIONr_angle_refined_deg1.3782.0114086
X-RAY DIFFRACTIONr_angle_other_deg0.7613.0016662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.845352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.81923.101129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86415545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1881525
X-RAY DIFFRACTIONr_chiral_restr0.0710.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213251
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021672
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9874.1011422
X-RAY DIFFRACTIONr_mcbond_other1.9764.0991419
X-RAY DIFFRACTIONr_mcangle_it3.296.1351768
X-RAY DIFFRACTIONr_mcangle_other3.2896.1341769
X-RAY DIFFRACTIONr_scbond_it2.1034.3041602
X-RAY DIFFRACTIONr_scbond_other2.1024.3041603
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3886.3452319
X-RAY DIFFRACTIONr_long_range_B_refined5.28432.2783348
X-RAY DIFFRACTIONr_long_range_B_other5.28332.2843348
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 111 -
Rwork0.272 993 -
obs--99.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.78880.02970.07910.3179-0.09780.4950.12110.12910.0372-0.05650.05360.0350.0057-0.1207-0.17470.04690.01430.00790.11910.04160.153826.89132.22131.204
21.74310.1674-1.19920.29940.24541.38250.0552-0.02340.0141-0.1366-0.0138-0.0676-0.1514-0.0057-0.04140.13380.01590.03890.0145-0.0330.16154.48227.30128.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A648 - 836
2X-RAY DIFFRACTION2B648 - 836

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