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- PDB-2rim: Crystal structure of Rtt109 -

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Basic information

Entry
Database: PDB / ID: 2rim
TitleCrystal structure of Rtt109
ComponentsRegulator of Ty1 transposition protein 109
KeywordsTRANSFERASE / Rtt109 structure / DNA damage / DNA repair / Nucleus / Transcription / Transcription regulation
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 / retrotransposon silencing ...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 / retrotransposon silencing / histone H3 acetyltransferase activity / 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
Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 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
DepositionOct 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulator of Ty1 transposition protein 109


Theoretical massNumber of molelcules
Total (without water)52,7481
Polymers52,7481
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Regulator of Ty1 transposition protein 109

A: Regulator of Ty1 transposition protein 109


Theoretical massNumber of molelcules
Total (without water)105,4952
Polymers105,4952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2370 Å2
ΔGint-12.3 kcal/mol
Surface area35410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.401, 69.233, 55.661
Angle α, β, γ (deg.)90.00, 94.93, 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: 52747.727 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: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q07794
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG550 MME, Ammonium citrate, glycerol, Tris, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 16, 2007
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. all: 29160 / Num. obs: 30288 / % possible obs: 0.989 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.098
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.7 % / Rsym value: 0.541 / % possible all: 0.971

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.035 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.197 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25907 1619 5.1 %RANDOM
Rwork0.21641 ---
obs0.21864 30288 94.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.504 Å2
Baniso -1Baniso -2Baniso -3
1-3.8 Å20 Å2-2.53 Å2
2---2.38 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 0 112 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223103
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.974193
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0835370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63523.551138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.23615563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9081520
X-RAY DIFFRACTIONr_chiral_restr0.0920.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022295
X-RAY DIFFRACTIONr_nbd_refined0.2090.21290
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22076
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4760.220
X-RAY DIFFRACTIONr_mcbond_it0.9551.51929
X-RAY DIFFRACTIONr_mcangle_it1.41923042
X-RAY DIFFRACTIONr_scbond_it1.89231341
X-RAY DIFFRACTIONr_scangle_it2.8614.51151
LS refinement shellResolution: 2.078→2.132 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 38 -
Rwork0.27 824 -
obs--34.66 %
Refinement TLS params.Method: refined / Origin x: 27.3684 Å / Origin y: 30.7892 Å / Origin z: 15.256 Å
111213212223313233
T-0.2673 Å2-0.0106 Å20.0117 Å2--0.1986 Å20.0246 Å2---0.2165 Å2
L0.6111 °2-0.4836 °20.5954 °2-2.924 °20.6506 °2--2.9743 °2
S-0.0485 Å °-0.0376 Å °0.0682 Å °0.0625 Å °0.0222 Å °0.08 Å °-0.0302 Å °-0.191 Å °0.0263 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 14222 - 163
2X-RAY DIFFRACTION1AA175 - 404196 - 425

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