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- PDB-2zfn: Self-acetylation mediated histone H3 lysine 56 acetylation by rtt109 -

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Basic information

Entry
Database: PDB / ID: 2zfn
TitleSelf-acetylation mediated histone H3 lysine 56 acetylation by rtt109
ComponentsRegulator of Ty1 transposition protein 109
KeywordsTRANSFERASE / histone h3 lysine 56 acetylation / DNA damage / DNA repair / Nucleus / Transcription / Transcription regulation
Function / homology
Function and homology information


H3 histone acetyltransferase complex / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / replication-born double-strand break repair via sister chromatid exchange / transposable element silencing / histone H3 acetyltransferase activity / protein-lysine-acetyltransferase activity / cellular response to stress / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity ...H3 histone acetyltransferase complex / regulation of double-strand break repair via nonhomologous end joining / maintenance of rDNA / replication-born double-strand break repair via sister chromatid exchange / transposable element silencing / histone H3 acetyltransferase activity / protein-lysine-acetyltransferase activity / cellular response to stress / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / protein modification process / nucleosome assembly / regulation of gene expression / DNA damage response / regulation of transcription by RNA polymerase II / chromatin / nucleus
Similarity search - Function
Histone acetyltransferase Rtt109 / : / Rtt109-type histone acetyltransferase (HAT) domain profile. / Histone acetyltransferase Rtt109/CBP / Histone acetylation protein / Histone acetylation protein
Similarity search - Domain/homology
ACETYL COENZYME *A / Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsYuan, Y.A.
CitationJournal: Structure / Year: 2008
Title: Structural insights into histone h3 lysine 56 acetylation by rtt109
Authors: Lin, C. / Yuan, Y.A.
History
DepositionJan 8, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of Ty1 transposition protein 109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9643
Polymers53,0621
Non-polymers9022
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.589, 68.612, 55.472
Angle α, β, γ (deg.)90.00, 95.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Regulator of Ty1 transposition protein 109 / Rtt109


Mass: 53062.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RTT109, KIM2, REM50 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07794
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG, Tris, Ammonium citrate, glycerol, ethylene glycol, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→73 Å / Num. obs: 41056 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.46 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2RIM

2rim


Resolution: 1.9→42.32 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.257 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.124 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22946 2178 5 %RANDOM
Rwork0.18497 ---
obs0.18718 41056 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.362 Å2
Baniso -1Baniso -2Baniso -3
1-4.69 Å20 Å2-1.49 Å2
2---2.56 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 57 215 3324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223176
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.9924297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6255371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64623.597139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2315559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1461520
X-RAY DIFFRACTIONr_chiral_restr0.1210.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022331
X-RAY DIFFRACTIONr_nbd_refined0.2360.21396
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22133
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2173
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.225
X-RAY DIFFRACTIONr_mcbond_it1.4291.51952
X-RAY DIFFRACTIONr_mcangle_it1.90423059
X-RAY DIFFRACTIONr_scbond_it2.85231419
X-RAY DIFFRACTIONr_scangle_it4.1544.51238
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 153 -
Rwork0.236 3021 -
obs--99.37 %
Refinement TLS params.Method: refined / Origin x: 27.1788 Å / Origin y: 30.5707 Å / Origin z: 15.1305 Å
111213212223313233
T-0.1102 Å2-0.0011 Å20.0047 Å2--0.0634 Å20.0091 Å2---0.0582 Å2
L0.5063 °2-0.1357 °20.1971 °2-1.5166 °20.2042 °2--1.8844 °2
S-0.0067 Å °0.0032 Å °0.0296 Å °-0.0349 Å °0.0246 Å °0.0781 Å °0.0036 Å °-0.1562 Å °-0.0179 Å °

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