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- PDB-8gq4: Histone acetyltransferase Rtt109 mutant-N195A -

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Basic information

Entry
Database: PDB / ID: 8gq4
TitleHistone acetyltransferase Rtt109 mutant-N195A
ComponentsHistone acetyltransferase RTT109
KeywordsTRANSFERASE / Histone acetyltransferase Rtt109
Function / homology
Function and homology information


regulation of phenotypic switching / negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / histone H3K56 acetyltransferase activity / phenotypic switching / filamentous growth / histone H3 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 RTT109
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsChen, Y.J. / Su, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31370735 China
CitationJournal: To Be Published
Title: Structure of Histone acetyltransferase Rtt109 mutant-N195A
Authors: Chen, Y.J. / Su, D.
History
DepositionAug 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone acetyltransferase RTT109


Theoretical massNumber of molelcules
Total (without water)41,8661
Polymers41,8661
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.768, 69.840, 54.585
Angle α, β, γ (deg.)90.000, 114.223, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Histone acetyltransferase RTT109


Mass: 41866.422 Da / Num. of mol.: 1 / Mutation: N195A,S321L,S336L,S339L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: RTT109 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5AAJ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Bis-Tris pH 6.0, 2% Tacsimate pH 6.0, 15~20% PEG 3350

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Data collection

DiffractionMean temperature: 126.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9754 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 34445 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 30.14 Å2 / Rmerge(I) obs: 0.185 / Net I/σ(I): 11.42
Reflection shellResolution: 1.77→1.82 Å / Rmerge(I) obs: 0.335 / Num. unique obs: 2832

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BXW

7bxw


Resolution: 1.77→49.78 Å / SU ML: 0.2031 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.3364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2341 1730 5.03 %
Rwork0.1884 32696 -
obs0.1908 34426 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.82 Å2
Refinement stepCycle: LAST / Resolution: 1.77→49.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2579 0 0 161 2740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122730
X-RAY DIFFRACTIONf_angle_d2.01183711
X-RAY DIFFRACTIONf_chiral_restr0.1011410
X-RAY DIFFRACTIONf_plane_restr0.0129471
X-RAY DIFFRACTIONf_dihedral_angle_d11.4744371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.820.29911300.29282652X-RAY DIFFRACTION97.58
1.82-1.880.29881730.27012700X-RAY DIFFRACTION100
1.88-1.950.27391430.2532716X-RAY DIFFRACTION100
1.95-2.030.25711470.24722716X-RAY DIFFRACTION100
2.03-2.120.28041480.23722702X-RAY DIFFRACTION100
2.12-2.230.26221300.21952753X-RAY DIFFRACTION100
2.23-2.370.25051330.22852724X-RAY DIFFRACTION100
2.37-2.560.23091370.21442726X-RAY DIFFRACTION99.97
2.56-2.810.2511270.20862747X-RAY DIFFRACTION100
2.81-3.220.24981180.1912781X-RAY DIFFRACTION100
3.22-4.060.22431700.15682711X-RAY DIFFRACTION100
4.06-49.780.20221740.14722768X-RAY DIFFRACTION99.97

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