PDB-3exn: Crystal structure of acetyltransferase from Thermus thermophilus HB8

ID or keywords:

Entry

Database: PDB / ID: 3exn

Title

Crystal structure of acetyltransferase from Thermus thermophilus HB8

Components

Probable acetyltransferase

Keywords

TRANSFERASE / acetyltransferase / GCN5-related N-acetyltransferase / MCSG / PSI / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

N-acetyltransferase activity
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.8 Å

Authors

Nocek, B. / Hatzos, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of acetyltransferase from Thermus thermophilus HB8
Authors: Nocek, B. / Hatzos, C. / Clancy, S. / Joachimiak, A.

History

Deposition	Oct 16, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 6, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3exn.cif.gz	50.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3exn.ent.gz	35.4 KB	Display	PDB format
PDBx/mmJSON format	3exn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3exn_validation.pdf.gz	700.8 KB	Display	wwPDB validaton report
Full document	3exn_full_validation.pdf.gz	702.9 KB	Display
Data in XML	3exn_validation.xml.gz	9.6 KB	Display
Data in CIF	3exn_validation.cif.gz	13 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ex/3exn ftp://data.pdbj.org/pub/pdb/validation_reports/ex/3exn	HTTPS FTP

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Related structure data

Similar structure data	6t08-2 5vxb-1 2n0t-d 2z93-1 1juq-1 1vjf-d 4ynl-2 1moz-2 4054 5vqj-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
Other databases	TargetDB: APC61206

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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)

Deposited unit

A: Probable acetyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	32.197, 52.408, 47.514
Angle α, β, γ (deg.)	90.00, 92.50, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

likely monomer

#1: Protein	Probable acetyltransferase Mass: 18037.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0176 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE(3) / References: UniProt: Q5SLW7
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula*: C₂₃H₃₈N₇O₁₇P₃S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.6 %
Crystal grow	Temperature: 289 K / pH: 7.5 Details: 0.1 M lithium Chloride 25% Peg 6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794
Detector	Type: SBC-3 / Detector: CCD / Date: Oct 13, 2008 / Details: MIRROR
Radiation	Monochromator: SI CRYSTALL 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 14476 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / R_merge(I) obs: 0.048 / Net I/σ(I): 26.3
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.194 / Mean I/σ(I) obs: 4.8 / % possible all: 94.9

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Processing

Software

Name	Version	Classification
SBC-Collect	Collect	data collection
HKL-3000		phasing
SHELX		model building
Coot		model building
MLPHARE		phasing
CCP4		model building
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.8→30 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.941 / SU B: 6.251 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21899	733	5.1 %	RANDOM
R_work	0.17604	-	-	-
obs	0.17825	13727	97.73 %	-
all	-	14457	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 8.301 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.28 Å²	0 Å²	2.4 Å²
2-	-	-1.73 Å²	0 Å²
3-	-	-	1.66 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1229	0	30	108	1367

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	1307
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	909
X-RAY DIFFRACTION	r_angle_refined_deg	1.589	2.009	1781
X-RAY DIFFRACTION	r_angle_other_deg	0.947	3	2192
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.26	5	157
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.316	21.803	61
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.809	15	207
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.095	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	192
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	1446
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	289
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.877	1.5	777
X-RAY DIFFRACTION	r_mcbond_other	0.265	1.5	311
X-RAY DIFFRACTION	r_mcangle_it	1.446	2	1247
X-RAY DIFFRACTION	r_scbond_it	2.318	3	530
X-RAY DIFFRACTION	r_scangle_it	3.702	4.5	532
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.798→1.845 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	35	-
R_work	0.232	857	-
obs	-	-	83.52 %

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	9.5477	0.365	0.9295	2.5251	-0.9501	0.4973	-0.2861	0.0721	0.0527	-0.1629	0.3162	0.1272	-0.0287	-0.1253	-0.03	0.2107	0.0067	-0.0049	0.2247	-0.0042	0.1944	19.9331	-2.912	10.1115
2	3.7869	3.7226	-1.5382	5.4683	-3.1943	2.4175	-0.2385	0.1226	-0.4562	-0.245	0.0567	-0.307	0.2788	0.0877	0.1817	0.2115	0.0215	0.0583	0.1822	-0.0106	0.2262	5.0018	-12.351	13.2131
3	4.1241	0.6255	-0.448	9.1384	2.3566	2.0972	-0.0933	-0.253	-0.0209	0.2133	0.081	-0.4354	0.0702	0.182	0.0123	0.1917	0.0092	-0.0099	0.184	-0.0022	0.1707	4.5674	-5.9751	22.083
4	2.6437	-2.563	-1.1995	4.9009	1.3746	0.666	0.2904	0.1163	0.1349	-0.1284	-0.288	-0.1122	0.0065	-0.0239	-0.0024	0.2211	0.0145	0.0309	0.1988	-0.0269	0.2124	2.1683	5.1463	22.2213
5	5.6657	-6.357	5.3248	14.9761	-10.8834	10.5982	0.1184	-0.0117	-0.2582	-0.0845	-0.0101	0.5632	0.2777	-0.3442	-0.1083	0.2301	-0.0234	0.0191	0.2161	-0.044	0.2232	-4.485	4.9431	24.1758
6	9.984	0.14	3.5107	8.9921	3.7161	9.0528	0.0176	-0.5396	0.0152	0.3604	-0.0219	0.5645	-0.0146	-0.3541	0.0043	0.1926	0.0061	0.0222	0.1937	-0.0045	0.1839	-3.9877	-6.8288	25.2465
7	2.5435	0.7028	3.6502	3.476	-2.0527	9.9374	-0.0612	-0.1259	-0.124	0.1132	0.0564	0.2488	0.08	-0.4192	0.0048	0.1636	-0.0102	0.0242	0.19	-0.0197	0.252	-6.7081	-11.8627	15.6614
8	6.1894	3.4178	-3.1211	12.9043	4.8738	6.1998	-0.2276	0.3945	-0.1731	-0.5226	-0.028	0.5849	-0.0292	-0.4378	0.2557	0.2035	0.0057	-0.0125	0.1992	0.0005	0.2053	-5.3347	-10.0767	4.8576
9	6.4424	-0.465	-0.169	3.9087	0.5071	2.2362	-0.1953	-0.1608	-0.4335	-0.0722	0.1683	-0.4608	0.1329	0.1854	0.027	0.1616	0.0164	0.0311	0.1782	0.0061	0.2403	10.7559	-7.4024	13.5006
10	5.3564	-0.8419	2.4894	1.7118	0.0792	3.0008	-0.0285	0.1646	-0.0772	-0.134	-0.1127	0.1509	0.0956	-0.1329	0.1411	0.1799	-0.0128	0.0017	0.1888	-0.0149	0.179	-2.8348	-3.4341	6.2722
11	5.9856	1.8872	3.5699	2.4297	2.4244	4.611	-0.0486	0.0916	0.093	-0.0905	0.0849	-0.0155	-0.1445	0.1258	-0.0363	0.1789	-0.007	0.0008	0.1713	0.0038	0.1673	4.0427	1.8462	10.8902
12	11.4339	2.5015	-3.7813	14.411	5.3567	6.6656	0.126	0.085	0.341	0.1024	-0.0443	-0.4325	-0.0992	0.4666	-0.0817	0.1735	-0.007	0.034	0.1859	-0.0034	0.218	13.4349	3.4996	7.5713
13	11.1821	5.2071	4.4192	6.7031	5.2099	10.2191	-0.0267	0.3059	-0.1047	-0.2735	0.0301	-0.2522	-0.0298	0.3644	-0.0034	0.1948	-0.0001	0.0139	0.1796	0.0079	0.1697	7.2922	-2.7157	0.9583
14	7.6671	0.2709	-0.9155	12.4447	3.5648	6.2956	0.2335	0.8376	-0.0803	-1.0544	-0.2565	0.4487	-0.1337	-0.3421	0.0231	0.3222	0.0537	-0.0533	0.3702	-0.0423	0.2193	-2.8579	-1.4531	-5.9563
15	3.533	1.2014	0.2639	5.9248	8.0026	13.4788	-0.0685	-0.3576	0.2882	0.3744	-0.2492	0.3599	-0.0245	-0.2595	0.3177	0.233	0.013	-0.0157	0.198	0.027	0.2047	-5.3094	8.2447	8.818
16	5.346	-3.2175	-6.251	6.4813	4.6696	9.6763	-0.0817	-0.3261	0.12	0.6165	0.1527	-0.2344	-0.2695	0.5169	-0.0709	0.2894	-0.0272	-0.0041	0.2129	0.0135	0.191	2.2731	12.7823	10.0196
17	5.2404	1.8987	-0.1319	3.8476	-2.0597	6.4279	0.1812	0.2514	-0.109	0.008	0.0338	-0.0937	-0.0341	-0.0551	-0.215	0.2078	-0.0096	0.0096	0.1854	0.0452	0.1658	2.0439	10.4121	1.1269
18	1.0975	-3.3924	3.2967	10.5815	-10.3097	10.0973	-0.1788	-0.1141	-0.1139	0.6193	0.5376	0.4789	-0.5835	-0.6845	-0.3589	0.2128	-0.0459	0.14	0.6864	-0.1152	0.5636	-10.0834	13.0765	3.2008
19	12.0095	1.9713	-4.2767	2.0913	-2.3485	15.4917	-0.0729	-0.3844	0.1297	0.4735	-0.0474	0.3785	-0.0022	-0.6265	0.1204	0.3328	-0.0325	0.1134	0.2801	-0.0251	0.3513	-9.9644	9.8341	8.7739
20	2.5931	2.15	2.053	9.1483	1.4449	1.6453	0.0844	0.3538	-0.1446	-0.3947	0.0366	-0.4636	0.1296	0.2786	-0.121	0.2015	0.0043	-0.0015	0.152	0.0361	0.0954	-0.732	6.1968	-2.4705

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 9
2	X-RAY DIFFRACTION	2	A	10 - 18
3	X-RAY DIFFRACTION	3	A	19 - 26
4	X-RAY DIFFRACTION	4	A	27 - 35
5	X-RAY DIFFRACTION	5	A	36 - 40
6	X-RAY DIFFRACTION	6	A	41 - 46
7	X-RAY DIFFRACTION	7	A	47 - 56
8	X-RAY DIFFRACTION	8	A	57 - 60
9	X-RAY DIFFRACTION	9	A	61 - 69
10	X-RAY DIFFRACTION	10	A	70 - 83
11	X-RAY DIFFRACTION	11	A	84 - 99
12	X-RAY DIFFRACTION	12	A	100 - 105
13	X-RAY DIFFRACTION	13	A	106 - 114
14	X-RAY DIFFRACTION	14	A	115 - 120
15	X-RAY DIFFRACTION	15	A	121 - 127
16	X-RAY DIFFRACTION	16	A	128 - 134
17	X-RAY DIFFRACTION	17	A	135 - 141
18	X-RAY DIFFRACTION	18	A	142 - 147
19	X-RAY DIFFRACTION	19	A	148 - 152
20	X-RAY DIFFRACTION	20	A	153 - 157

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