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

ID or keywords:

Entry

Database: PDB / ID: 7bwz

Title

Crystal structure of RTT109 from CANDIDA ALBICANS

Components

Histone acetyltransferase RTT109

Keywords

TRANSFERASE / 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

Biological species

Candida albicans (yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.77 Å

Authors

Chen, Y.P. / Lei, J.H. / Su, D.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Crystal structure of RTT109 from CANDIDA ALBICANS
Authors: Chen, Y.P. / Lei, J.H. / Su, D.

History

Deposition	Apr 16, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 21, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: 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
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	7bwz_validation.pdf.gz	433.5 KB	Display	wwPDB validaton report
Full document	7bwz_full_validation.pdf.gz	436.9 KB	Display
Data in XML	7bwz_validation.xml.gz	15.7 KB	Display
Data in CIF	7bwz_validation.cif.gz	22.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bw/7bwz ftp://data.pdbj.org/pub/pdb/validation_reports/bw/7bwz	HTTPS FTP

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Related structure data

Related structure data	7bx0S S: Starting model for refinement
Similar structure data	7bx0-d 4tkn-1 1thy-d 1t6c-d 3byx-d 7bxw-d 3nc5-1 5iqb-4 1f0o-d 3wec-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#7 - Jul 2000 Nucleosome similarity (1) #122 - Feb 2010 Enhanceosome similarity (4) #67 - Jul 2005 TATA-Binding Protein similarity (1)

Deposited unit

A: Histone acetyltransferase RTT109

41.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

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 number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

#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 Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.41 %
Crystal grow	Temperature: 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

Diffraction

Mean temperature: 193 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U1 / Wavelength: 0.975 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.975 Å / Relative weight: 1

Reflection

Resolution: 1.77→50 Å / Num. obs: 34042 / % possible obs: 99.2 % / Redundancy: 7.2 % / B_iso Wilson estimate: 33.16 Å² / R_merge(I) obs: 0.096 / R_pim(I) all: 0.038 / R_rim(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 (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.77-1.82	5.5	0.404	2622	0.931	0.18	0.444	0.403	92.9
1.82-1.88	6.3	0.32	2850	0.956	0.135	0.349	0.456	99.1
1.88-1.95	6.8	0.268	2786	0.971	0.11	0.291	0.523	99.8
1.95-2.03	6.9	0.22	2862	0.975	0.09	0.239	0.578	99.9
2.03-2.12	7.1	0.187	2842	0.983	0.075	0.202	0.643	99.9
2.12-2.23	7.7	0.156	2839	0.988	0.06	0.167	0.728	100
2.23-2.37	7.7	0.136	2857	0.991	0.053	0.147	0.781	100
2.37-2.55	7.2	0.119	2859	0.991	0.048	0.129	0.864	99.9
2.55-2.81	7.9	0.105	2843	0.992	0.04	0.112	0.941	100
2.81-3.22	7.6	0.086	2891	0.994	0.034	0.092	1.037	100
3.22-4.05	7.8	0.079	2870	0.994	0.031	0.084	1.065	100
4.05-50	7.4	0.083	2921	0.993	0.033	0.09	1.052	99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
HKL-2000	V1.0	data scaling
PDB_EXTRACT	3.25	data extraction

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.1929	1710	5.03 %
R_work	0.1732	-	-
obs	0.1742	34017	99.12 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 44.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.77→49.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2582	0	0	216	2798

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0086	2735
X-RAY DIFFRACTION	f_angle_d	1.1392	3715
X-RAY DIFFRACTION	f_chiral_restr	0.0617	409
X-RAY DIFFRACTION	f_plane_restr	0.0047	469
X-RAY DIFFRACTION	f_dihedral_angle_d	16.9933	1031

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.77-1.82	0.2494	121	0.2454	2460	X-RAY DIFFRACTION	91.59
1.82-1.88	0.2459	167	0.2242	2679	X-RAY DIFFRACTION	99.06
1.88-1.95	0.2562	143	0.2012	2657	X-RAY DIFFRACTION	99.72
1.95-2.03	0.2133	149	0.201	2701	X-RAY DIFFRACTION	99.82
2.03-2.12	0.2239	144	0.195	2695	X-RAY DIFFRACTION	99.86
2.12-2.23	0.1945	128	0.1864	2735	X-RAY DIFFRACTION	100
2.23-2.37	0.2216	134	0.1847	2721	X-RAY DIFFRACTION	99.96
2.37-2.55	0.1853	138	0.1881	2724	X-RAY DIFFRACTION	99.9
2.55-2.81	0.2262	125	0.1904	2718	X-RAY DIFFRACTION	100
2.81-3.21	0.2241	121	0.1877	2771	X-RAY DIFFRACTION	99.97
3.21-4.05	0.1692	167	0.1606	2704	X-RAY DIFFRACTION	100
4.05-49.79	0.1736	173	0.1479	2742	X-RAY DIFFRACTION	99.45

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.18569692741	-0.677076322447	-0.0246517634374	3.38191149955	-0.111926241224	1.91002000053	0.026633539506	-0.516800247948	0.124797944908	0.330540981104	0.0120298903092	-0.0354630191261	0.00962940328493	-0.105535222638	-0.111827631223	0.288709559353	-0.0560062845471	0.0104105455645	0.255597221917	0.008112093421	0.186375352355	-9.56906531731	0.796500332397	-8.40038257361
2	3.10276698216	-0.443586180725	-0.348718139054	2.56367425333	0.0349208421805	1.17306114066	0.0530657718568	-0.106926969489	0.170791319603	0.337765259419	-0.0585999566383	0.031162295671	-0.118592874656	0.0525354996185	0.0178922855152	0.280369262033	-0.0356871214681	0.00937219513604	0.243464996197	-0.00751022964493	0.188090767342	-13.310959999	-1.59183147919	-6.95973211443
3	4.91262995883	2.42124482747	-0.398190987811	2.23744036821	-0.470128375005	0.23319558709	-0.0839120024542	0.286365134253	-0.491619557976	0.16972102424	0.153775769656	-0.557492127054	0.00617750924227	0.184301904286	-0.0811348526716	0.335624479659	0.016876912669	-0.0332070929448	0.365094329001	-0.0109369832166	0.379397229075	-2.30702296716	-17.6801244354	-10.1395584609
4	2.88214783436	-0.61728765563	0.268316890497	2.96529592695	-1.04286236855	5.77818702558	-0.0682435929737	0.015140092592	-0.463495581306	0.153446077059	0.0968944531693	0.327315700177	0.502428959623	-0.237587605703	-0.0208980287272	0.260104722704	-0.0502542094515	0.041329736343	0.239529135192	0.00784218606054	0.314809857854	-21.8398008777	-21.0677379223	-9.49913485194
5	2.5677327053	-0.409757240499	-0.870098377909	3.13603926887	1.04480613025	2.21956800165	0.0147295382707	0.388068787814	-0.133565380648	-0.322185344542	-0.0368431736988	0.133892708401	-0.135698782364	-0.114293959982	0.0156062435241	0.29270317597	-0.0166812227827	-0.0201572570567	0.302220857446	-0.03104409686	0.25124518377	-19.1569832954	-14.2437078147	-24.2050788851
6	4.36267235962	-0.0593939095754	0.408467188459	2.69598958412	0.183790161862	0.225643498961	0.0831455738155	-0.187494891696	0.362239472351	0.166344126277	-0.0968637723851	-0.342609640869	-0.0713803316278	0.123653887865	-0.00807611189997	0.354325879549	-0.0599558600941	-0.0215544400268	0.366689694415	0.00946708773082	0.319735566923	-1.27129187425	3.030629534	-9.54312694056

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 53 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 54 through 177 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 178 through 213 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 214 through 253 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 254 through 310 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 311 through 358 )

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