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- PDB-8gq3: RTT109 mutant from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 8gq3
TitleRTT109 mutant from Candida albicans
ComponentsHistone acetyltransferase RTT109
KeywordsTRANSFERASE / histone acetyltransferase
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: 1.767 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: Crystal structure of RTT109 mutant-Y183A from Candida albicans
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

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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)41,8881
Polymers41,8881
Non-polymers00
Water5,242291
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)51.249, 69.335, 54.538
Angle α, β, γ (deg.)90.000, 115.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone acetyltransferase RTT109


Mass: 41888.422 Da / Num. of mol.: 1 / Mutation: Y183A,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 / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 6.0, 2% Tacsimate pH 6.0 and 15~20% PEG3350

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Data collection

DiffractionMean temperature: 126.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.767→50 Å / Num. obs: 33734 / % possible obs: 98.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.043 / Rrim(I) all: 0.119 / Χ2: 0.928 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.825.80.47124530.8980.20.5140.50987.1
1.82-1.887.10.3928630.9410.1540.420.5699.9
1.88-1.957.50.32127860.9570.1250.3450.659100
1.95-2.037.40.2528470.9720.0980.2690.716100
2.03-2.127.30.21128330.9760.0830.2270.829100
2.12-2.237.90.17528050.9840.0660.1880.95100
2.23-2.377.70.15628510.9870.060.1671.046100
2.37-2.557.30.13628280.9870.0540.1461.142100
2.55-2.817.90.12428440.9890.0470.1331.216100
2.81-3.227.60.10928560.9910.0420.1171.169100
3.22-4.057.90.10228590.9910.0380.1091.058100
4.05-507.50.0929090.9920.0350.0971.07199.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BXW

7bxw


Resolution: 1.767→49.359 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2018 1707 5.06 %
Rwork0.1617 31997 -
obs0.1637 33704 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.04 Å2 / Biso mean: 36.7914 Å2 / Biso min: 15.04 Å2
Refinement stepCycle: final / Resolution: 1.767→49.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 15 291 2869
Biso mean--41.76 43.43 -
Num. residues----313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.767-1.8190.27381330.248247893
1.819-1.87770.28471440.20092678100
1.8777-1.94480.22821300.17752660100
1.9448-2.02270.21781340.172676100
2.0227-2.11470.21341380.16982680100
2.1147-2.22620.20811240.16132692100
2.2262-2.36570.21540.16482668100
2.3657-2.54840.20231500.16282659100
2.5484-2.80480.19051240.17672704100
2.8048-3.21060.21461600.17142691100
3.2106-4.04470.18841480.14762689100
4.0447-49.3590.18961680.14592722100
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)
10.7753-0.2651-0.11570.7916-0.29790.51740.11880.608-0.1065-0.470.1028-0.05140.0150.15090.06970.36550.0489-0.0740.337-0.02490.20762.614735.50871.2476
20.3209-0.451-0.37611.8074-0.10710.44730.1383-0.04580.20650.0322-0.1259-0.25540.01160.0591-0.00020.21460.0165-0.0120.2207-0.01960.215515.214635.967613.9345
30.3925-0.61390.23591.0309-0.15150.05110.0532-0.08930.1287-0.1534-0.0464-0.12270.02910.00430.00010.1589-0.00730.01690.2189-0.00630.174913.592331.955310.2001
40.1937-0.3730.11710.7161-0.0570.4796-0.06730.2221-0.171-0.49610.00920.24320.0688-0.1148-0.00260.30730.0347-0.06930.2527-0.02750.22561.957925.19641.2176
50.9096-0.1193-0.29890.31370.04410.95120.07430.01540.2574-0.2355-0.0419-0.2144-0.1410.0366-0.00040.26070.00690.06740.19590.01240.288219.826339.60417.085
60.5167-0.58960.260.8014-0.15150.11770.0736-0.1481-0.3099-0.17240.03580.29770.0972-0.09080.00050.2303-0.0094-0.00940.24390.00860.28922.093317.09739.9211
70.4160.0674-0.14250.43040.36420.33420.0022-0.0791-0.2845-0.1383-0.16-0.39890.30630.2391-0.00040.29040.01650.04930.21510.00170.249319.657912.24758.8749
80.6046-0.2892-0.31190.2948-0.24030.6997-0.02410.0309-0.208-0.17070.0505-0.15890.1560.304600.2380.02370.03650.2617-0.01470.293123.960916.133310.1997
90.7559-0.0742-0.54711.5388-0.52870.5957-0.0219-0.1611-0.06260.12130.022-0.0894-0.0890.0155-0.00050.19780.0064-0.00770.21440.02480.197718.807720.855124.0417
100.86850.27620.63251.3529-0.32360.59870.11230.3050.366-0.1946-0.1895-0.0298-0.1938-0.2787-0.00010.25340.04310.00610.22490.01260.23558.44839.45468.6465
110.2518-0.01370.02420.1849-0.190.21450.03030.11350.0455-0.02970.01550.6167-0.1299-0.38110.00150.23780.07370.02220.3470.03310.463-12.313133.659211.3147
12222.000128.483420.4492-0.222-0.7213-1.7627-0.49112.0245-2.1263-0.34880.16760.84220.3066-0.01620.50120.39071.0811-9.392745.47848.0069
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 24 )A0 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 53 )A25 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 83 )A54 - 83
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 106 )A84 - 106
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 177 )A107 - 177
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 213 )A178 - 213
7X-RAY DIFFRACTION7chain 'A' and (resid 214 through 236 )A214 - 236
8X-RAY DIFFRACTION8chain 'A' and (resid 237 through 253 )A237 - 253
9X-RAY DIFFRACTION9chain 'A' and (resid 254 through 310 )A254 - 310
10X-RAY DIFFRACTION10chain 'A' and (resid 311 through 339 )A311 - 339
11X-RAY DIFFRACTION11chain 'A' and (resid 340 through 356 )A340 - 356
12X-RAY DIFFRACTION12chain 'A' and (resid 357 through 357 )A357

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