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- PDB-5zb9: Crystal structure of Rtt109 from Aspergillus fumigatus -

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Basic information

Entry
Database: PDB / ID: 5zb9
TitleCrystal structure of Rtt109 from Aspergillus fumigatus
ComponentsDNA damage response protein Rtt109, putative
KeywordsTRANSFERASE / Histone / acetylation / DNA replication / nucleosome assembly / DNA damage
Function / homology
Function and homology information


histone H3K56 acetyltransferase activity / histone acetyltransferase / DNA damage response / regulation of DNA-templated transcription / 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
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.502 Å
AuthorsZhang, L. / Serra-Cardona, A. / Zhou, H. / Wang, M. / Yang, N. / Zhang, Z. / Xu, R.M.
Funding support China, United States, 7items
OrganizationGrant numberCountry
NSFC31210103914 China
NSFC31521002 China
NSFC31430018 China
Ministry of Science and Technology of China2015CB856200 China
Chinese Academy of SciencesXDB08010100 China
Beijing Municipal Science and Technology ProjectZ171100000417001 China
NIHGM118015 United States
CitationJournal: Cell / Year: 2018
Title: Multisite Substrate Recognition in Asf1-Dependent Acetylation of Histone H3 K56 by Rtt109.
Authors: Zhang, L. / Serra-Cardona, A. / Zhou, H. / Wang, M. / Yang, N. / Zhang, Z. / Xu, R.M.
History
DepositionFeb 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 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: DNA damage response protein Rtt109, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7772
Polymers59,6851
Non-polymers921
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint0 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.185, 92.019, 98.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA damage response protein Rtt109, putative


Mass: 59684.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_5G09540 / Plasmid: pET-28a-smt3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q4WUS9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: 100mM sodium cacodylate, pH 6.4, 16% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 26067 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.17 Å2 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.057 / Rrim(I) all: 0.151 / Χ2: 0.97 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.597.10.72625660.80.290.7830.97100
2.59-2.6970.51225450.8780.2080.5530.975100
2.69-2.826.60.39925630.9170.1670.4330.98100
2.82-2.9670.29825990.9550.1210.3220.982100
2.96-3.157.20.22425560.9690.0890.2420.984100
3.15-3.397.10.16126030.9830.0650.1741.002100
3.39-3.736.60.12225830.9860.0510.1320.974100
3.73-4.277.10.10826230.9910.0430.1161.002100
4.27-5.386.70.09526460.9910.0390.1030.939100
5.38-506.50.08927830.9910.0380.0970.88899.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZFN

2zfn


Resolution: 2.502→49.185 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.57
RfactorNum. reflection% reflection
Rfree0.2092 1319 5.08 %
Rwork0.1662 --
obs0.1684 25943 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 139.67 Å2 / Biso mean: 40.9286 Å2 / Biso min: 11.36 Å2
Refinement stepCycle: final / Resolution: 2.502→49.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 6 195 3356
Biso mean--28.26 40.39 -
Num. residues----402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053270
X-RAY DIFFRACTIONf_angle_d0.8464452
X-RAY DIFFRACTIONf_chiral_restr0.035489
X-RAY DIFFRACTIONf_plane_restr0.004582
X-RAY DIFFRACTIONf_dihedral_angle_d13.3941200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5016-2.60170.28811380.23282606274496
2.6017-2.72010.28061490.21126762825100
2.7201-2.86350.25561460.207427192865100
2.8635-3.04290.22121410.187727042845100
3.0429-3.27780.24491630.179427312894100
3.2778-3.60750.20551560.161727132869100
3.6075-4.12930.17341310.148527762907100
4.1293-5.20160.17011360.135428012937100
5.2016-49.19450.19671590.15828983057100

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