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- PDB-3cz7: Molecular Basis for the Autoregulation of the Protein Acetyl Tran... -

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Basic information

Entry
Database: PDB / ID: 3cz7
TitleMolecular Basis for the Autoregulation of the Protein Acetyl Transferase Rtt109
ComponentsRegulator of Ty1 transposition protein 109
KeywordsREPLICATION / Chromatin Stability
Function / homology
Function and homology information


histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / replication-born double-strand break repair via sister chromatid exchange / histone H3 acetyltransferase activity ...histone H3K23 acetyltransferase activity / histone H3K56 acetyltransferase activity / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / regulation of double-strand break repair via nonhomologous end joining / histone H3K9 acetyltransferase activity / maintenance of rDNA / replication-born double-strand break repair via sister chromatid exchange / histone H3 acetyltransferase activity / retrotransposon silencing / histone H3K27 acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / histone acetyltransferase / protein modification process / nucleosome assembly / regulation of gene expression / DNA damage response / chromatin / regulation of transcription by RNA polymerase II / 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 / SAD / Resolution: 2 Å
AuthorsHoelz, A. / Stavropoulos, P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Molecular basis for the autoregulation of the protein acetyl transferase Rtt109
Authors: Stavropoulos, P. / Nagy, V. / Blobel, G. / Hoelz, A.
History
DepositionApr 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen

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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)42,9912
Polymers42,1811
Non-polymers8101
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.782, 68.886, 55.241
Angle α, β, γ (deg.)90.00, 106.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Regulator of Ty1 transposition protein 109


Mass: 42181.465 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 / Cell line (production host): BL21-CodonPlus(DE3)-RIL / Production host: Escherichia coli (E. coli) / References: UniProt: Q07794
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.72 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 12% (w/v) PEG 4,000, 1 mM ZnCl2, and 100 mM Sodium Acetate, pH 4.4, temperature 294K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X3A / Wavelength: 0.9798
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 55305 / Observed criterion σ(I): 3

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.85 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflection
Rfree0.189 1496 5.1 %
Rwork0.156 --
obs0.158 29452 100 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 22.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å20.71 Å2
2---0.93 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 51 276 3287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223083
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.994181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36823.813139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98715539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7311519
X-RAY DIFFRACTIONr_chiral_restr0.1150.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022301
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.21424
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22121
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2265
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1921.51885
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69322972
X-RAY DIFFRACTIONr_scbond_it2.5431376
X-RAY DIFFRACTIONr_scangle_it3.9514.51209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å
RfactorNum. reflection% reflection
Rfree0.206 111 -
Rwork0.154 2061 -
obs--100 %
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)
11.340.1941-0.14430.97430.36651.4927-0.02240.0108-0.12430.0510.02710.05360.1742-0.0645-0.00470.01180.00420.0036-0.04370.0104-0.014118.23894.387713.5727
20.52290.1899-0.16551.2682-0.06220.9704-0.0033-0.04770.0034-0.01410.05040.0165-0.0029-0.02-0.0472-0.00670.0024-0.0055-0.0157-0.0008-0.007522.40567.872810.6712
30.9524-0.4496-0.44131.45660.65561.56940.11410.2831-0.1357-0.3433-0.14990.0933-0.0628-0.24060.03580.05440.0122-0.01870.0454-0.0309-0.001221.58684.91-8.3176
41.12840.0842-0.41380.74470.47351.62960.0593-0.18530.1610.1644-0.01030.0544-0.0774-0.0601-0.049-0.0035-0.00170.0138-0.0449-0.0144-0.00717.35813.162819.7168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 792 - 79
2X-RAY DIFFRACTION2AA80 - 19880 - 159
3X-RAY DIFFRACTION3AA199 - 277160 - 238
4X-RAY DIFFRACTION4AA285 - 365246 - 326

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