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- PDB-3qm0: Crystal structure of RTT109-AC-CoA complex -

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Basic information

Entry
Database: PDB / ID: 3qm0
TitleCrystal structure of RTT109-AC-CoA complex
ComponentsHistone acetyltransferase RTT109
KeywordsTRANSFERASE / RTT109 / HISTONE ACETYLTRANSFERASE (HAT) / P300/CBP / HISTONE H3 K56 / GENOME STABILITY / DNA DAMAGE / DNA REPAIR / NUCLEUS / TRANSCRIPTION / TRANSCRIPTION REGULATION / Histone Acetyltransferase (HAT) fold / Histone Acetyltransferase / Vps75 histone chaperone / auto-acetylation / Lys290
Function / homology
Function and homology information


: / : / : / histone H3K23 acetyltransferase activity / : / histone H3K56 acetyltransferase activity / : / H3 histone acetyltransferase complex / DNA replication-dependent chromatin disassembly / : ...: / : / : / 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 / peptidyl-lysine acetylation / 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 / protein acetylation / histone acetyltransferase / 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 / MAD / Resolution: 3.1 Å
AuthorsTang, Y. / Marmorstein, R.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Fungal Rtt109 histone acetyltransferase is an unexpected structural homolog of metazoan p300/CBP.
Authors: Tang, Y. / Holbert, M.A. / Wurtele, H. / Meeth, K. / Rocha, W. / Gharib, M. / Jiang, E. / Thibault, P. / Verrault, A. / Cole, P.A. / Marmorstein, R.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 16, 2011ID: 3D35
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 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: Histone acetyltransferase RTT109
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8604
Polymers44,6491
Non-polymers1,2113
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)233.791, 233.791, 233.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein Histone acetyltransferase RTT109 / Regulator of Ty1 transposition protein 109


Mass: 44649.348 Da / Num. of mol.: 1 / Fragment: RTT109 DELTA(130-179) / Mutation: DELTA(130-179) mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: KIM2, L1377, REM50, RTT109, YLL002W / Plasmid: GST_PCDF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: Q07794, histone acetyltransferase
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


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


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: reservoir solution contains 12.5% (v/v) PEG4000, 100 mM Hepes. Protein (10 mg/ml) in 20 mM Hepes, 150 mM NaCl, and 5 mM BME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0072, 1.0090
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 13, 2007 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00721
21.0091
ReflectionResolution: 3.1→50 Å / Num. obs: 18820 / % possible obs: 100 % / Observed criterion σ(I): -3.5 / Redundancy: 45.5 % / Biso Wilson estimate: 55.5 Å2 / Rsym value: 0.123 / Net I/σ(I): 51.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 44.9 % / Mean I/σ(I) obs: 14.5 / Rsym value: 0.414 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→50 Å / Occupancy max: 1 / Occupancy min: 0.3 / Isotropic thermal model: ISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: This entry is to replace 3D35 due to an incorrect chirality of the ACO ligand.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 941 -5%
Rwork0.194 ---
obs-18820 100 %-
Displacement parametersBiso max: 90.61 Å2 / Biso mean: 37.9944 Å2 / Biso min: 6.1 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 53 28 2973
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.48

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