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- PDB-7bwz: Crystal structure of RTT109 from CANDIDA ALBICANS -

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Basic information

Entry
Database: PDB / ID: 7bwz
TitleCrystal structure of RTT109 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
Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsChen, Y.P. / Lei, J.H. / Su, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)31370735 China
CitationJournal: To Be Published
Title: Crystal structure of RTT109 from CANDIDA ALBICANS
Authors: Chen, Y.P. / Lei, J.H. / Su, D.
History
DepositionApr 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 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


Theoretical massNumber of molelcules
Total (without water)41,8331
Polymers41,8331
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16300 Å2
Unit cell
Length a, b, c (Å)51.422, 69.594, 54.733
Angle α, β, γ (deg.)90.000, 114.542, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Histone acetyltransferase RTT109


Mass: 41833.348 Da / Num. of mol.: 1 / Mutation: S321L,S336L,S339L
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 42.41 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Bis-Tris pH 6.0, 15~20% PEG 3350

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.975 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 34042 / % possible obs: 99.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 33.16 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.038 / Rrim(I) all: 0.104 / Χ2: 0.78 / Net I/σ(I): 5.3 / Num. measured all: 244106
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.825.50.40426220.9310.180.4440.40392.9
1.82-1.886.30.3228500.9560.1350.3490.45699.1
1.88-1.956.80.26827860.9710.110.2910.52399.8
1.95-2.036.90.2228620.9750.090.2390.57899.9
2.03-2.127.10.18728420.9830.0750.2020.64399.9
2.12-2.237.70.15628390.9880.060.1670.728100
2.23-2.377.70.13628570.9910.0530.1470.781100
2.37-2.557.20.11928590.9910.0480.1290.86499.9
2.55-2.817.90.10528430.9920.040.1120.941100
2.81-3.227.60.08628910.9940.0340.0921.037100
3.22-4.057.80.07928700.9940.0310.0841.065100
4.05-507.40.08329210.9930.0330.091.05299.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000V1.0data scaling
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BX0

7bx0


Resolution: 1.77→49.79 Å / SU ML: 0.1892 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.6513
RfactorNum. reflection% reflection
Rfree0.1929 1710 5.03 %
Rwork0.1732 --
obs0.1742 34017 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.6 Å2
Refinement stepCycle: LAST / Resolution: 1.77→49.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 0 216 2798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00862735
X-RAY DIFFRACTIONf_angle_d1.13923715
X-RAY DIFFRACTIONf_chiral_restr0.0617409
X-RAY DIFFRACTIONf_plane_restr0.0047469
X-RAY DIFFRACTIONf_dihedral_angle_d16.99331031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.820.24941210.24542460X-RAY DIFFRACTION91.59
1.82-1.880.24591670.22422679X-RAY DIFFRACTION99.06
1.88-1.950.25621430.20122657X-RAY DIFFRACTION99.72
1.95-2.030.21331490.2012701X-RAY DIFFRACTION99.82
2.03-2.120.22391440.1952695X-RAY DIFFRACTION99.86
2.12-2.230.19451280.18642735X-RAY DIFFRACTION100
2.23-2.370.22161340.18472721X-RAY DIFFRACTION99.96
2.37-2.550.18531380.18812724X-RAY DIFFRACTION99.9
2.55-2.810.22621250.19042718X-RAY DIFFRACTION100
2.81-3.210.22411210.18772771X-RAY DIFFRACTION99.97
3.21-4.050.16921670.16062704X-RAY DIFFRACTION100
4.05-49.790.17361730.14792742X-RAY DIFFRACTION99.45
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)
13.18569692741-0.677076322447-0.02465176343743.38191149955-0.1119262412241.910020000530.026633539506-0.5168002479480.1247979449080.3305409811040.0120298903092-0.03546301912610.00962940328493-0.105535222638-0.1118276312230.288709559353-0.05600628454710.01041054556450.2555972219170.0081120934210.186375352355-9.569065317310.796500332397-8.40038257361
23.10276698216-0.443586180725-0.3487181390542.563674253330.03492084218051.173061140660.0530657718568-0.1069269694890.1707913196030.337765259419-0.05859995663830.031162295671-0.1185928746560.05253549961850.01789228551520.280369262033-0.03568712146810.009372195136040.243464996197-0.007510229644930.188090767342-13.310959999-1.59183147919-6.95973211443
34.912629958832.42124482747-0.3981909878112.23744036821-0.4701283750050.23319558709-0.08391200245420.286365134253-0.4916195579760.169721024240.153775769656-0.5574921270540.006177509242270.184301904286-0.08113485267160.3356244796590.016876912669-0.03320709294480.365094329001-0.01093698321660.379397229075-2.30702296716-17.6801244354-10.1395584609
42.88214783436-0.617287655630.2683168904972.96529592695-1.042862368555.77818702558-0.06824359297370.015140092592-0.4634955813060.1534460770590.09689445316930.3273157001770.502428959623-0.237587605703-0.02089802872720.260104722704-0.05025420945150.0413297363430.2395291351920.007842186060540.314809857854-21.8398008777-21.0677379223-9.49913485194
52.5677327053-0.409757240499-0.8700983779093.136039268871.044806130252.219568001650.01472953827070.388068787814-0.133565380648-0.322185344542-0.03684317369880.133892708401-0.135698782364-0.1142939599820.01560624352410.29270317597-0.0166812227827-0.02015725705670.302220857446-0.031044096860.25124518377-19.1569832954-14.2437078147-24.2050788851
64.36267235962-0.05939390957540.4084671884592.695989584120.1837901618620.2256434989610.0831455738155-0.1874948916960.3622394723510.166344126277-0.0968637723851-0.342609640869-0.07138033162780.123653887865-0.008076111899970.354325879549-0.0599558600941-0.02155444002680.3666896944150.009467087730820.319735566923-1.271291874253.030629534-9.54312694056
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 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 253 )
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 310 )
6X-RAY DIFFRACTION6chain 'A' and (resid 311 through 358 )

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