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- PDB-7c3o: Crystal structure of TT109 from CANDIDA ALBICANS -

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Basic information

Entry
Database: PDB / ID: 7c3o
TitleCrystal structure of TT109 from CANDIDA ALBICANS
ComponentsHistone acetyltransferase RTT109
KeywordsTRANSFERASE / HISTONE / ACETYLATION / DNA REPLICATION / NUCLEOSOME ASSEMBLY / DNA DAMAGE
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 / DNA replication-dependent chromatin disassembly / histone H3 acetyltransferase activity / filamentous growth / histone acetyltransferase / DNA damage response ...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 / DNA replication-dependent chromatin disassembly / histone H3 acetyltransferase activity / filamentous growth / 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
ACETYL COENZYME *A / DI(HYDROXYETHYL)ETHER / Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsChen, Y.P. / Lei, J.H. / Lu, D.R. / Su, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31370735 China
CitationJournal: To Be Published
Title: Crystal structure of TT109 from CANDIDA ALBICANS
Authors: Chen, Y.P. / Lei, J.H. / Lu, D.R. / Su, D.
History
DepositionMay 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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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)43,0465
Polymers41,9321
Non-polymers1,1144
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-2 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.754, 70.036, 54.559
Angle α, β, γ (deg.)90.000, 114.316, 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: 41932.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: RTT109, CAALFM_CR00410WA, CaO19.7491 / Plasmid: pET-Duet1 vector / Production host: Escherichia coli (E. coli) / References: UniProt: Q5AAJ8, histone acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 107314 / % possible obs: 98.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.47 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.85
Reflection shellResolution: 1.89→1.97 Å / Num. unique obs: 107314 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BXW

7bxw


Resolution: 1.89→25.82 Å / SU ML: 0.1742 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.7444
RfactorNum. reflection% reflection
Rfree0.1919 1408 5.03 %
Rwork0.1654 --
obs0.1667 28013 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38.32 Å2
Refinement stepCycle: LAST / Resolution: 1.89→25.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2599 0 71 229 2899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012765
X-RAY DIFFRACTIONf_angle_d1.21833744
X-RAY DIFFRACTIONf_chiral_restr0.0702406
X-RAY DIFFRACTIONf_plane_restr0.0046461
X-RAY DIFFRACTIONf_dihedral_angle_d14.25731030
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.960.24871440.20432477X-RAY DIFFRACTION93.74
1.96-2.040.22731420.18112632X-RAY DIFFRACTION98.37
2.04-2.130.21751540.17932650X-RAY DIFFRACTION98.32
2.13-2.240.21751300.16552652X-RAY DIFFRACTION98.79
2.24-2.380.19291580.17192663X-RAY DIFFRACTION98.98
2.38-2.570.1941520.17272657X-RAY DIFFRACTION99.08
2.57-2.820.23651180.18252704X-RAY DIFFRACTION99.19
2.82-3.230.18031330.17852716X-RAY DIFFRACTION99.51
3.23-4.070.19491480.15112697X-RAY DIFFRACTION99.82
4.07-25.820.1521290.15072757X-RAY DIFFRACTION99.31
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)
13.06690244686-0.291667597221-0.472879424793.278994477480.05748439622951.751143074120.0138955289916-0.457611288739-0.1462020635240.286939772346-0.01435342056230.0187923144591-0.0449210982498-0.0520067168601-0.1063506854250.18391661532-0.05554210762380.01443710238230.1806794650430.02293338032490.1179468753664.939634523070.22795708076416.4967447928
22.00366751665-0.0806604076883-0.2531129794342.405332812210.1939180592521.043917342220.0592057722162-0.0321452561573-0.02848337052070.227505982195-0.0518607796621-0.103618281704-0.01531173106730.116293970816-0.001456564789360.170021898544-0.0280235135521-0.01349973323370.1788123493860.01593115947530.1111437530464.96176777678-6.9839509539416.7635292349
33.12015645593-1.149887114260.4646604732823.53721368623-1.576409013614.834646131430.001253361048040.0554801761638-0.4338399256290.154539598160.01856647755150.3559752078560.451991623937-0.210568083409-0.0212846018280.185600155966-0.05161572790430.04334827452190.173564294502-0.007041184832460.26201814481-7.17574594966-21.645204772115.4796579296
41.684640106370.241667189538-0.2585398383342.459988124850.341039194640.822778528551-0.03987498488760.159348174061-0.0567743460502-0.0254292787876-0.01334518936830.167784638656-0.0451030610888-0.00817958180470.09669255823220.201865843122-0.00130695691662-0.008825568175820.244345444433-0.007645644385120.193486650651-4.10026212743-10.6929989335.66058203606
52.46988422713-2.013275345831.822205698882.26611779132-1.103372202152.62258625740.03160836097640.1384076792770.176370645213-0.2153746169290.0505047314465-0.455532251858-0.2051109396580.188647903681-0.01476233482880.199652195646-0.06448080559850.01743434554490.2476459431270.04235268548470.35711117570621.64557698961.395340660911.1185402845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 213 )
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 253 )
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 326 )
5X-RAY DIFFRACTION5chain 'A' and (resid 327 through 359 )

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