PDB-5jq4: Structure of a GNAT acetyltransferase SACOL1063 from Staphylococc...

ID or keywords:

Entry

Database: PDB / ID: 5jq4

Title

Structure of a GNAT acetyltransferase SACOL1063 from Staphylococcus aureus

Components

Acetyltransferase SACOL1063

Keywords

TRANSFERASE / acetyltransferase / Gcn5-related N-acetyltransferase / GNAT / protein acetylation / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Majorek, K.A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: Biochim.Biophys.Acta / Year: 2016
Title: Insight into the 3D structure and substrate specificity of previously uncharacterized GNAT superfamily acetyltransferases from pathogenic bacteria.
Authors: Majorek, K.A. / Osinski, T. / Tran, D.T. / Revilla, A. / Anderson, W.F. / Minor, W. / Kuhn, M.L.

History

Deposition	May 4, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 29, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 16, 2016	Group: Database references
Revision 1.2	Dec 7, 2016	Group: Other
Revision 1.3	Apr 13, 2022	Group: Database references / Structure summary / Category: audit_author / citation_author / database_2 Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 23, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5jq4.cif.gz	137.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5jq4.ent.gz	108.5 KB	Display	PDB format
PDBx/mmJSON format	5jq4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5jq4_validation.pdf.gz	443 KB	Display	wwPDB validaton report
Full document	5jq4_full_validation.pdf.gz	443.7 KB	Display
Data in XML	5jq4_validation.xml.gz	14.8 KB	Display
Data in CIF	5jq4_validation.cif.gz	21.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jq/5jq4 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/5jq4	HTTPS FTP

-
Related structure data

Related structure data	5jphC C: citing same article (ref.)
Similar structure data	2rhd-d 4m91-d 5bob-3 3bfk-5 5zx8-d 2c24-2 5eg9-2 5wop-1 5c6h-2 2g0b-6 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP00739

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #97 - Jan 2008 Circadian Clock Proteins similarity (4) #190 - Oct 2015 Two-component Systems similarity (1)

Deposited unit

A: Acetyltransferase SACOL1063

B: Acetyltransferase SACOL1063

hetero molecules

34.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Acetyltransferase SACOL1063

hetero molecules

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

2

B: Acetyltransferase SACOL1063

hetero molecules

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

3

A: Acetyltransferase SACOL1063

B: Acetyltransferase SACOL1063

hetero molecules

A: Acetyltransferase SACOL1063

B: Acetyltransferase SACOL1063

hetero molecules

defined by software
69.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	129.453, 33.839, 67.529
Angle α, β, γ (deg.)	90.000, 109.510, 90.000
Int Tables number	5
Space group name H-M	C121

-
Protein , 1 types, 2 molecules AB

#1: Protein	Acetyltransferase SACOL1063 / GCN5-related N-acetyltransferase / GNAT Mass: 17171.229 Da / Num. of mol.: 2 / Mutation: V28I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: SACOL1063 / Production host: Escherichia coli (E. coli) References: UniProt: Q5HH30, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

#1: Protein

Acetyltransferase SACOL1063 / GCN5-related N-acetyltransferase / GNAT

Mass: 17171.229 Da / Num. of mol.: 2 / Mutation: V28I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Staphylococcus aureus (bacteria) / Strain: COL / Gene: SACOL1063 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q5HH30, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

-
Non-polymers , 5 types, 218 molecules

#2: Chemical	ChemComp-SCN / THIOCYANATE ION Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-UNX / UNKNOWN ATOM OR ION Num. of mol.: 3 / Source method: obtained synthetically
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.4 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium thiocyanate and 20% PEG3350

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97923 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2012 / Details: mirrors

Radiation

Monochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97923 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 25666 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / B_iso Wilson estimate: 22.1 Å² / R_merge(I) obs: 0.1 / R_sym value: 0.1 / Net I/av σ(I): 26.061 / Net I/σ(I): 10.7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.8-1.83	4.1	0.666	2.1	1	100
1.83-1.86	4.1	0.552		1	100
1.86-1.9	4.2	0.436		1	100
1.9-1.94	4.2	0.367		1	100
1.94-1.98	4.1	0.3		1	100
1.98-2.03	4.2	0.269		1	100
2.03-2.08	4.2	0.22		1	100
2.08-2.13	4.2	0.181		1	100
2.13-2.2	4.2	0.177		1	99.9
2.2-2.27	4.2	0.152		1	100
2.27-2.35	4.2	0.144		1	100
2.35-2.44	4.2	0.129		1	100
2.44-2.55	4.2	0.119		1	100
2.55-2.69	4.2	0.115		1	100
2.69-2.86	4.2	0.107		1	100
2.86-3.08	4.2	0.101		1	100
3.08-3.39	4.1	0.084		1	100
3.39-3.88	4.1	0.067		1	99.9
3.88-4.88	4.1	0.065		1	99.8
4.88-50	4	0.089		1	99

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
HKL-2000		data scaling
REFMAC	5.8.0135	refinement
PDB_EXTRACT	3.2	data extraction
HKL-3000		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→50 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.946 / SU B: 6.014 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.127
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2118	1309	5.1 %	RANDOM
R_work	0.1801	-	-	-
obs	0.1819	24356	99.15 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 86.89 Å² / B_iso mean: 27.375 Å² / B_iso min: 9.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.66 Å²	0 Å²	-0.54 Å²
2-	-	1.4 Å²	0 Å²
3-	-	-	-0.29 Å²

Refinement step

Cycle: final / Resolution: 1.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2293	0	17	211	2521
B_iso mean	-	-	30.06	36.51	-
Num. residues	-	-	-	-	288

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	2426
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2317
X-RAY DIFFRACTION	r_angle_refined_deg	1.796	1.976	3260
X-RAY DIFFRACTION	r_angle_other_deg	2.003	3	5348
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.789	5	305
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.673	24.836	122
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.414	15	411
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.796	15	15
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	347
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	2786
X-RAY DIFFRACTION	r_gen_planes_other	0.009	0.02	563
X-RAY DIFFRACTION	r_mcbond_it	0.557	0.718	1191
X-RAY DIFFRACTION	r_mcbond_other	0.535	0.713	1187
X-RAY DIFFRACTION	r_mcangle_it	0.936	1.067	1493

LS refinement shell

Resolution: 1.804→1.85 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.288	78	-
R_work	0.244	1609	-
all	-	1687	-
obs	-	-	90.12 %

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	4.0441	-0.4944	-1.7927	2.5605	-1.2236	6.9731	-0.1591	-0.3341	-0.0469	0.1995	0.0927	-0.1632	0.4386	0.5711	0.0665	0.1576	0.0584	0.0137	0.2133	0.019	0.1048	18.064	-1.163	23.165
2	7.9269	-2.5834	6.9898	9.3277	0.7657	7.2855	0.3844	0.7022	-0.8685	0.1073	0.403	0.0444	0.3523	0.868	-0.7874	0.3443	-0.0472	-0.1282	0.1644	0.0187	0.5231	9.212	-11.684	25.871
3	4.1566	-0.0925	0.434	4.2334	0.8053	8.0788	0.0546	-0.1549	-0.1546	0.0022	-0.0826	-0.0834	0.2083	0.3231	0.0281	0.156	0.01	0.0248	0.1793	0.0274	0.1726	15.557	-0.271	20.264
4	1.8926	-0.1891	0.368	1.8083	0.0369	5.7556	0.0512	-0.1019	0.0166	0.0396	0.0048	0.0576	0.1212	-0.1332	-0.056	0.1855	-0.0209	0.0338	0.1953	0.0118	0.2141	7.451	2.924	18.89
5	2.9777	-0.0356	0.5934	2.6931	0.9597	5.3168	0.141	0.1998	0.3261	-0.0981	-0.0373	-0.0986	-0.2863	0.1044	-0.1038	0.2058	-0.0146	0.044	0.1367	0.0102	0.1947	9.677	9.385	11.534
6	2.8272	1.7211	-0.4667	2.489	0.1323	5.3479	-0.1094	-0.1812	0.0713	-0.0569	0.0434	-0.1621	-0.2418	-0.0611	0.066	0.154	-0.0071	-0.0094	0.1261	0.003	0.2095	-3.813	6.889	18.966
7	8.3202	1.7315	0.9302	8.9199	-1.0498	5.5132	0.179	-0.3261	-0.2449	0.4787	-0.3296	-0.3659	-0.08	0.3585	0.1506	0.1905	-0.0322	-0.0069	0.1353	0.0019	0.1945	-12.971	-2.908	14.997
8	14.5612	11.131	-3.6503	20.3314	-6.7087	7.8408	-0.061	0.6017	0.5542	-0.1744	0.3297	0.315	-0.3166	-0.3525	-0.2686	0.1903	0.0194	0.0149	0.1537	0.0003	0.2543	-0.572	8.152	10.683
9	1.1766	1.2221	0.0947	4.578	0.5143	1.5203	0.0094	0.0816	0.0473	-0.081	0.0315	-0.1314	-0.0528	-0.0505	-0.0409	0.1689	-0	0.0017	0.1188	-0.015	0.1934	-29.33	-6.965	-0.548
10	1.3276	-0.349	0.6253	1.9934	-0.1195	0.9038	0.038	0.0571	-0.1269	0.0617	-0.0207	-0.0706	0.1043	0.0883	-0.0172	0.1853	-0.0004	0.0045	0.0931	-0.0068	0.2019	-20.296	-10.735	6.548
11	3.1768	0.6699	-1.2863	2.2456	-0.5179	3.8958	0.0445	-0.0781	0.0722	0.1448	-0.0147	0.0709	-0.0171	-0.0385	-0.0299	0.1998	-0.0047	-0.0038	0.1151	-0.014	0.1931	-24.494	-3.193	11.691
12	8.3404	3.5913	-1.9419	2.9816	-1.8232	3.3104	0.0095	0.0369	0.1522	0.0793	0.0443	0.2168	-0.0774	-0.1699	-0.0537	0.2026	0.0052	0.0122	0.102	-0.006	0.2131	-31.988	2.154	10.167
13	2.8088	0.163	-0.3161	1.0949	-0.2092	0.4377	-0.0266	-0.0544	0.0784	0.0947	-0.0304	-0.032	-0.063	-0.0092	0.057	0.1975	-0.0061	0.0118	0.1198	-0.0039	0.159	-20.81	5.032	17.798
14	0.6319	-0.5869	2.5589	1.4233	-5.5804	22.1301	0.0221	-0.0071	0.0713	0.0384	-0.0579	0.0128	-0.177	0.3065	0.0357	0.2093	0.0016	0.0178	0.167	0.0072	0.2214	-25.049	5.567	28.364
15	11.3092	-0.292	-0.3772	18.6551	-2.393	11.3199	0.0738	-0.2402	-0.3303	-0.4228	0.1055	-0.012	1.4188	0.8276	-0.1794	0.2142	0.0951	-0.0313	0.172	0.0073	0.1514	-19.946	-4.266	35.701
16	17.8995	-5.8436	5.672	5.965	-2.6288	6.2836	-0.2133	-0.1242	0.3378	0.1158	0.1867	0.2272	-0.4631	-0.431	0.0265	0.2539	0.0254	0.0156	0.1218	0.0091	0.1853	-30.795	5.609	19.537

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 22
2	X-RAY DIFFRACTION	2	A	23 - 34
3	X-RAY DIFFRACTION	3	A	35 - 55
4	X-RAY DIFFRACTION	4	A	56 - 85
5	X-RAY DIFFRACTION	5	A	86 - 103
6	X-RAY DIFFRACTION	6	A	104 - 121
7	X-RAY DIFFRACTION	7	A	122 - 133
8	X-RAY DIFFRACTION	8	A	134 - 141
9	X-RAY DIFFRACTION	9	B	-2 - 10
10	X-RAY DIFFRACTION	10	B	11 - 53
11	X-RAY DIFFRACTION	11	B	54 - 81
12	X-RAY DIFFRACTION	12	B	82 - 100
13	X-RAY DIFFRACTION	13	B	101 - 117
14	X-RAY DIFFRACTION	14	B	118 - 126
15	X-RAY DIFFRACTION	15	B	127 - 133
16	X-RAY DIFFRACTION	16	B	134 - 143

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 218 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 218 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 218 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi