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- PDB-7bxw: Crystal structure ofF RTT109 FROM Candida albicans -

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Basic information

Entry
Database: PDB / ID: 7bxw
TitleCrystal structure ofF 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 / phenotypic switching / filamentous growth / histone H3 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity ...regulation of phenotypic switching / negative regulation of filamentous growth of a population of unicellular organisms / filamentous growth of a population of unicellular organisms / phenotypic switching / filamentous growth / histone H3 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 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: 1.77629297561 Å
AuthorsLei, J.H. / Chen, Y.P. / Lu, D.R. / Su, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31370735 China
Citation
Journal: To be published
Title: Crystal structure ofF RTT109 FROM Candida albicans
Authors: Su, D. / Hu, Q.
#1: Journal: J. Biol. Chem / Year: 2011
Title: Structure and histone binding properties of the Vps75-Rtt109 chaperone-lysine acetyltransferase complex
Authors: Su, D. / Hu, Q.
History
DepositionApr 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1473
Polymers42,0291
Non-polymers1182
Water5,080282
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-0 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.479, 69.564, 54.59
Angle α, β, γ (deg.)90.0, 114.705, 90.0
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Histone acetyltransferase RTT109


Mass: 42028.785 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) / 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.: 282 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
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: 80 K / Ambient temp details: 77 / 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: 1.77→50 Å / Num. obs: 33152 / % possible obs: 98.4 % / Redundancy: 7.6 % / Biso Wilson estimate: 22.0078106624 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.03 / Rrim(I) all: 0.084 / Χ2: 0.802 / Net I/σ(I): 5.9 / Num. measured all: 252953
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.77-1.87.10.29815990.9590.1170.3210.49496.1
1.8-1.837.60.25916480.9690.0990.2770.50797.3
1.83-1.877.70.22416270.9770.0850.240.55597.3
1.87-1.917.60.20416180.9810.0780.2190.57597.9
1.91-1.957.70.18516490.9810.0710.1980.62997.9
1.95-1.997.60.1716280.9860.0650.1820.63497.9
1.99-2.047.20.15116570.9870.0590.1630.69497.6
2.04-2.17.50.14616370.9890.0560.1560.7198
2.1-2.1680.13616490.990.0510.1450.80398.2
2.16-2.237.90.12116430.9910.0450.130.8298.3
2.23-2.317.80.11716460.9910.0440.1250.83398.4
2.31-2.47.60.10716630.9920.0410.1150.84498.8
2.4-2.517.20.09716620.9940.0380.1050.86698.9
2.51-2.647.90.09516640.9930.0360.1010.88799.2
2.64-2.8180.08716810.9960.0320.0930.89698.8
2.81-3.037.90.07716780.9960.0290.0820.97999.1
3.03-3.337.30.07116810.9950.0280.0771.11399.4
3.33-3.818.10.06616850.9970.0240.071.08799.6
3.81-4.87.50.06216970.9970.0230.0660.99699.7
4.8-507.60.05917400.9960.0220.0631.02799.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000V1.0data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77629297561→49.5934705553 Å / SU ML: 0.150737498595 / Cross valid method: THROUGHOUT / σ(F): 1.38249054184 / Phase error: 20.9278720425
RfactorNum. reflection% reflection
Rfree0.201180048755 1684 5.08009291381 %
Rwork0.162715104119 31465 -
obs0.164712564487 33149 98.0536575265 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.5105658116 Å2
Refinement stepCycle: LAST / Resolution: 1.77629297561→49.5934705553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 8 282 2846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01347736424462707
X-RAY DIFFRACTIONf_angle_d1.392573292813673
X-RAY DIFFRACTIONf_chiral_restr0.0579216328439404
X-RAY DIFFRACTIONf_plane_restr0.00724300433389466
X-RAY DIFFRACTIONf_dihedral_angle_d14.29356386531019
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7763-1.82860.2459482172181280.194595429672435X-RAY DIFFRACTION91.7651271035
1.8286-1.88760.2294163521691350.182285788252592X-RAY DIFFRACTION97.6369495166
1.8876-1.95510.2228312888251390.1795760721582606X-RAY DIFFRACTION97.8609625668
1.9551-2.03330.2476454294241270.1806365649062611X-RAY DIFFRACTION97.6810560114
2.0333-2.12590.2278032916571380.1796228889032626X-RAY DIFFRACTION98.327997154
2.1259-2.2380.221976717931270.1622880943032626X-RAY DIFFRACTION98.0064079744
2.238-2.37820.1766540745451460.1654250354052635X-RAY DIFFRACTION98.8272921109
2.3782-2.56180.1981813352031470.1619528452892608X-RAY DIFFRACTION98.7809250627
2.5618-2.81960.195213546651250.1718718858382683X-RAY DIFFRACTION99.0126939351
2.8196-3.22750.2169113212331570.1694137802972663X-RAY DIFFRACTION99.3307502642
3.2275-4.0660.2032407296711490.1521798375182668X-RAY DIFFRACTION99.5758218452
4.066-49.590.1724846897341660.1477334384112712X-RAY DIFFRACTION99.7573656846

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