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- PDB-7bx1: Crystal structure of RTT109 from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 7bx1
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 / 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
ACETAMIDE / Histone acetyltransferase RTT109
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 RTT109 from Candida albicans
Authors: Chen, Y.P. / Lei, J.H. / Lu, D.R. / Su, D.
History
DepositionApr 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1753
Polymers42,0571
Non-polymers1182
Water5,405300
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint6 kcal/mol
Surface area15930 Å2
Unit cell
Length a, b, c (Å)51.317, 69.422, 54.486
Angle α, β, γ (deg.)90.000, 114.402, 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: 42056.531 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 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q5AAJ8, histone acetyltransferase
#2: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
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: 77.36 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 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 331312 / % possible obs: 97.9 % / Observed criterion σ(I): 1.7 / Redundancy: 7 % / Biso Wilson estimate: 19.07 Å2 / CC1/2: 0.99 / Net I/σ(I): 3.8
Reflection shellResolution: 1.58→1.63 Å / Num. unique obs: 331312 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000v1.0data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→49.62 Å / SU ML: 0.1504 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.5952
RfactorNum. reflection% reflection
Rfree0.1945 2451 5.21 %
Rwork0.1824 --
obs0.183 47038 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.77 Å2
Refinement stepCycle: LAST / Resolution: 1.58→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2609 0 8 300 2917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382836
X-RAY DIFFRACTIONf_angle_d0.70613859
X-RAY DIFFRACTIONf_chiral_restr0.0499417
X-RAY DIFFRACTIONf_plane_restr0.0039491
X-RAY DIFFRACTIONf_dihedral_angle_d18.50671064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.610.30551190.2562276X-RAY DIFFRACTION89.17
1.61-1.640.24691440.23762402X-RAY DIFFRACTION96.51
1.64-1.670.22291410.22962424X-RAY DIFFRACTION96.61
1.67-1.710.22991490.22472444X-RAY DIFFRACTION97.04
1.71-1.760.21871370.2082452X-RAY DIFFRACTION97.08
1.76-1.80.22571350.20452462X-RAY DIFFRACTION97.3
1.8-1.860.23871710.20042415X-RAY DIFFRACTION97.51
1.86-1.920.20281390.20112506X-RAY DIFFRACTION97.67
1.92-1.980.2061690.19822423X-RAY DIFFRACTION97.81
1.98-2.060.22671470.18992484X-RAY DIFFRACTION98.39
2.06-2.160.1821440.18452471X-RAY DIFFRACTION98.12
2.16-2.270.2161380.1812502X-RAY DIFFRACTION98.65
2.27-2.410.20041290.18822487X-RAY DIFFRACTION98.53
2.41-2.60.19911050.19342556X-RAY DIFFRACTION98.92
2.6-2.860.1772930.19022589X-RAY DIFFRACTION99.3
2.86-3.280.19471320.18232522X-RAY DIFFRACTION99.36
3.28-4.130.15421630.1582533X-RAY DIFFRACTION99.63
4.13-49.620.1854960.15922639X-RAY DIFFRACTION99.6
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)
13.52052535577-1.70916468042.482109445232.60120227495-1.955703818164.1879208326-0.00133318231949-0.62285758754-0.06570912120740.4874299686510.171818733037-0.0555234294283-0.0403844329460.0276896900096-0.1259712072970.265029441463-0.0249292615424-0.03974063879250.2732807599990.005425534451890.135777647716-2.401375242590.687807739813-1.40863975176
22.105931874690.1874527297-0.3343549659462.424875979640.0661061032430.8650961007670.0518680012502-0.02585569453930.1404585999060.244507435964-0.07701407832380.158162694532-0.08828348938310.01115089634330.01266032699680.159823041365-0.02041514703550.03771648796110.1120520795490.002642718225930.103091819206-13.5202872311-1.23051989521-9.06100291758
34.583866696922.44933901431-0.5735428955492.65245990154-0.4176943184550.207705845324-0.134703641090.232212586296-0.5890019075580.08293752575510.12273275043-0.4926358994420.06274433399590.1376301595130.05537243123550.1853041329740.004346897032460.003604566924530.181296909098-0.006710921137160.259238321504-2.35187701486-17.5132941665-10.1465669328
42.4645802028-0.60125347548-1.629200869382.49131169815-1.147468485754.56894723014-0.09081838241010.0524513978617-0.4118628053990.0979798457587-0.07432253872890.3458682811240.469944718326-0.1436038546740.1601475745710.184253192229-0.02762462279870.05279940949320.142501170367-0.001035864622090.260445561297-19.9706449338-22.5544490727-8.75898319577
52.37648822338-0.1064355706891.265976649113.16786076695-2.5163026527.988645255090.00610553705226-0.00507957613657-0.4273426637390.09105005439960.1578785962140.277693078070.204493341929-0.427246939451-0.1665793835080.134179483471-0.0178630203350.06670702682310.150851914053-0.01151249613890.210915711295-24.5927862733-18.7171683974-10.268126291
62.120700235010.231981575508-0.2844171091882.352568591710.4069829719010.945837096977-0.03247818536460.178381676539-0.02749636326950.00514887798565-0.004762629776150.200057610711-0.02660386384580.01896884498740.06773477880990.1403200940020.0006096452714020.01946232730540.132027810937-0.004521563421680.129913865445-18.6938944822-9.6499125906-18.6161614757
73.55930904016-2.634931722731.620980621642.34567396971-1.078315582521.815844209720.01183213601440.1835909835130.362806820779-0.0680791437942-0.024163650155-0.515009140715-0.2213676776980.188063456372-0.01105336302160.191445867884-0.0604464732410.03935802172580.1968046649940.03986290279520.3268137035566.627453025051.87101375527-13.589698456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 177 )
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 213 )
4X-RAY DIFFRACTION4chain 'A' and (resid 214 through 236 )
5X-RAY DIFFRACTION5chain 'A' and (resid 237 through 253 )
6X-RAY DIFFRACTION6chain 'A' and (resid 254 through 326 )
7X-RAY DIFFRACTION7chain 'A' and (resid 327 through 359 )

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