PDB-1nsl: Crystal structure of Probable acetyltransferase

ID or keywords:

Entry

Database: PDB / ID: 1nsl

Title

Crystal structure of Probable acetyltransferase

Components

Probable acetyltransferase

Keywords

TRANSFERASE / Structural genomics / Hexamer / Alpha-Beta / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Function and homology information

N-terminal peptidyl-serine acetylation / peptide-alanine-alpha-N-acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.7 Å

Authors

Brunzelle, J.S. / Korolev, S.V. / Wu, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: Proteins / Year: 2004
Title: Crystal structure of Bacillus subtilis YdaF protein: A putative ribosomal N-acetyltransferase
Authors: Brunzelle, J.S. / Wu, R. / Korolev, S.V. / Collart, F.R. / Joachimiak, A. / Anderson, W.F.

History

Deposition	Jan 27, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1nsl.cif.gz	214.8 KB	Display	PDBx/mmCIF format
PDB format	pdb1nsl.ent.gz	183.2 KB	Display	PDB format
PDBx/mmJSON format	1nsl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1nsl_validation.pdf.gz	485.1 KB	Display	wwPDB validaton report
Full document	1nsl_full_validation.pdf.gz	541.8 KB	Display
Data in XML	1nsl_validation.xml.gz	43.9 KB	Display
Data in CIF	1nsl_validation.cif.gz	59.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ns/1nsl ftp://data.pdbj.org/pub/pdb/validation_reports/ns/1nsl	HTTPS FTP

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Related structure data

Similar structure data	6hvq-d 6hui-d 2f7n-1 6hv1-d 6lf0-d 3h4r-1 6hx2-d 2bk6-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: APC1068

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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

B: Probable acetyltransferase

C: Probable acetyltransferase

D: Probable acetyltransferase

E: Probable acetyltransferase

F: Probable acetyltransferase

hetero molecules

128 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	59.339, 134.185, 91.062
Angle α, β, γ (deg.)	90.00, 104.08, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Probable acetyltransferase Mass: 21250.785 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YDAF / Production host: Escherichia coli (E. coli) / References: UniProt: P96579
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal

Density Matthews: 2.76 Å³/Da / Density % sol: 57.33 %

Crystal grow

*PLUS

pH: 6 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Chemical formula	Details
1	8 mg/ml	protein	1	drop
2	10 %	PEG6000	1	reservoir
4	0.1 M		1	reservoir	NaCl
3		sodium potassium phosphate	1	reservoir		pH6.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.984 Å
Detector	Type: SBC-2 / Detector: CCD / Details: mirrors
Radiation	Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.984 Å / Relative weight: 1
Reflection	Resolution: 2.45→50 Å / Num. obs: 47865 / Observed criterion σ(I): -3
Reflection	PLUS Highest resolution: 2.45 Å / Num. obs: 48725 / % possible obs: 100 % / Redundancy: 2.4 % / R_merge(I) obs*: 0.102

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Processing

Software

Name	Version	Classification
REFMAC	5	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
SOLVE		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.7→20 Å / Cor.coef. F_o:F_c: 0.908 / Cor.coef. F_o:F_c free: 0.902 / SU B: 13.195 / SU ML: 0.274 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27817	3120	8.5 %	RANDOM
R_work	0.25625	-	-	-
obs	0.25808	33550	96.81 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 30.671 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.15 Å²	0 Å²	2.13 Å²
2-	-	-1.14 Å²	0 Å²
3-	-	-	-1.97 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8589	0	6	19	8614

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.023	0.021	8804
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.462	1.95	11882
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.902	3	1074
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	21.456	15	1604
X-RAY DIFFRACTION	r_chiral_restr	0.211	0.2	1283
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	6678
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.325	0.3	4150
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.237	0.5	657
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.416	0.3	30
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.65	0.5	5
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_mcbond_it	0.767	1.5	5327
X-RAY DIFFRACTION	r_mcangle_it	1.461	2	8486
X-RAY DIFFRACTION	r_scbond_it	2.635	3	3477
X-RAY DIFFRACTION	r_scangle_it	4.194	4.5	3396
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.7→2.769 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.36	239
R_work	0.323	2183

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	7.7327	1.9669	-2.2756	7.8577	-2.3885	10.2554	0.1152	0.7855	0.1079	0.0815	0.093	1.0038	0.0812	-1.8968	-0.2082	0.0987	-0.043	-0.1153	0.8567	0.0071	0.3589	-24.3307	-21.1722	-25.3894
2	4.7837	0.9638	1.6088	3.7401	1.9983	13.9723	-0.3573	0.6577	-0.0912	0.0478	0.0372	0.1552	0.1973	-0.5213	0.3201	0.0983	-0.0694	-0.0316	0.516	0.0333	0.4407	-21.2403	-25.579	-17.1505
3	15.671	3.3405	6.1878	9.2029	3.6631	14.4163	-0.7363	1.511	-1.4593	0.5027	0.3427	-0.0892	1.5247	0.41	0.3936	0.4653	-0.1063	0.1421	0.4939	-0.082	0.5111	-19.1196	-33.7285	-16.6227
4	5.1043	0.3238	-1.4608	5.3186	1.8525	7.9647	0.0309	0.1779	-0.3174	0.3972	-0.1419	0.383	0.596	-0.6035	0.1111	0.4278	-0.1497	0.0385	0.3697	0.0627	0.4079	-26.0373	-27.8858	-4.6475
5	10.5257	-0.7835	-1.1644	9.1581	2.0344	11.6596	0.1389	-0.7143	-0.117	0.0705	0.1688	-1.8559	-0.0371	2.4467	-0.3076	0.1085	0.048	-0.0935	0.947	-0.0749	0.6999	2.9855	-21.1948	-27.4652
6	3.7921	-2.4625	2.7358	8.2668	-4.6177	13.8019	-0.4023	-0.4364	-0.158	-0.004	0.126	-0.9274	0.1387	0.744	0.2763	0.0206	0.0499	0.0542	0.57	-0.1088	0.5445	-0.6307	-22.7069	-36.6764
7	13.5932	-6.864	3.1818	8.7583	-3.9356	7.0191	-0.1172	-0.6458	-1.1173	-0.6682	0.3175	-0.1352	1.0546	0.315	-0.2003	0.3195	0.0642	0.0922	0.5775	-0.0561	0.7109	-3.2752	-29.9126	-39.9774
8	11.1327	0.3789	-3.4096	8.8676	1.0136	9.2642	0.1711	-0.0267	-0.4316	-0.7615	0.4293	-1.5339	0.0285	1.289	-0.6004	0.3379	-0.0122	0.1724	0.6026	-0.2528	0.6103	4.281	-21.0165	-49.2646
9	8.6268	-1.2758	0.9845	8.7856	2.2714	6.448	-0.367	0.1163	0.3303	-0.5566	-0.0478	0.6492	-0.3452	-0.892	0.4148	0.4583	0	-0.0352	0.3967	-0.1328	0.5014	-26.5064	14.204	-11.7508
10	11.6155	3.2585	-1.9418	5.3381	0.2069	3.8491	-0.1162	-0.1635	-0.0395	-0.1127	-0.0644	0.272	-0.1867	-0.1612	0.1806	0.5363	0.096	-0.046	0.3544	-0.1687	0.4302	-20.0999	20.6274	-8.2373
11	12.8764	1.7443	-4.3727	0.4114	-0.0584	4.7305	0.1563	-1.4597	-0.0589	0.316	-0.2562	0.3854	0.0701	0.4446	0.0999	0.5484	0.0929	-0.069	0.4722	-0.2194	0.5166	-20.0616	23.8075	-0.4448
12	4.7392	0.8581	-1.6781	4.1559	-1.1755	9.2023	-0.1302	-0.0614	0.83	0.0037	0.0766	0.2284	-0.5384	0.1092	0.0536	0.4792	0.0454	-0.1001	0.2953	-0.1977	0.6158	-16.3321	33.3706	-11.2403
13	8.4468	-1.0153	0.5312	7.2403	0.338	9.4965	0.0188	-0.9039	-0.1576	0.7219	-0.0467	-0.9775	0.2408	1.2204	0.0279	0.6114	-0.0574	-0.0291	0.6354	0.0635	0.5423	-8.1817	-0.3806	2.8882
14	7.1999	3.8586	1.1532	7.3615	1.1893	9.5947	0.0118	0.0887	0.1394	0.2241	0.1739	-0.2634	-0.5447	0.7984	-0.1857	0.4997	0.0299	0.0116	0.3887	0.0567	0.3182	-16.9725	-4.8429	4.2937
15	12.4337	2.569	6.9925	2.2622	4.5106	18.2809	-0.3767	-0.6643	0.941	0.2224	-0.1746	0.2091	-1.209	-0.1903	0.5513	0.7077	0.0031	0.0562	0.3988	-0.0252	0.3854	-22.7736	-2.2757	9.8468
16	1.8223	1.1423	-1.5519	6.753	2.1189	7.1034	-0.0573	-0.6062	-0.2649	0.8581	0.0591	0.0139	0.5116	0.2088	-0.0018	0.5395	-0.004	-0.0682	0.409	0.1323	0.3057	-21.3681	-17.0147	7.9516
17	7.1323	-0.0834	-2.5934	12.6691	1.3182	7.8323	-0.3209	0.784	-0.0576	-1.7382	-0.2456	2.2081	-0.4294	-0.981	0.5665	0.8129	0.0042	-0.2375	0.5459	-0.1079	0.7494	-11.9457	8.1639	-46.3786
18	5.956	-4.8096	0.8873	14.4632	1.3579	7.6251	-0.3958	-0.229	0.1576	-1.3435	0.5569	0.1113	-0.8039	-0.0968	-0.1611	0.7735	-0.2104	0.0286	0.4934	-0.1046	0.4285	-3.2259	4.3245	-49.2672
19	11.2686	-8.5978	1.5742	21.3279	-1.0202	6.2297	-0.6534	0.2998	0.9466	-2.6264	0.9908	-1.8426	-2.8997	0.8932	-0.3373	1.594	-0.4726	0.4283	0.5403	-0.1508	0.5554	2.8195	8.3058	-53.6053
20	4.2031	0.2657	1.2041	11.6163	3.5854	10.6443	-0.2629	0.6867	0.0164	-2.113	0.7347	-0.7655	-1.3439	0.6702	-0.4718	1.061	-0.2334	0.2965	0.6094	-0.1612	0.3623	0.5929	-6.054	-57.1752
21	9.2423	0.3032	0.5759	10.1255	-2.571	8.8128	-0.307	-0.7648	0.2842	0.5922	-0.1798	-0.9139	-0.2859	1.3508	0.4869	0.4211	-0.0464	0.0298	0.5954	-0.0117	0.5966	7.2949	16.8238	-28.1035
22	10.7816	-1.9707	-2.5472	4.4816	0.8712	4.195	-0.195	-0.1239	-0.4226	-0.2822	-0.0112	-0.3147	-0.3121	0.6355	0.2062	0.4831	-0.1509	-0.0838	0.4051	-0.0013	0.4586	0.9062	24.3646	-29.1335
23	28.5173	3.0181	1.1787	6.6183	1.2956	3.1595	-0.6001	1.8067	-0.2228	-1.0804	0.4272	-0.2017	-0.8222	0.7062	0.1729	0.5993	-0.1904	-0.1077	0.4466	0.0421	0.5447	0.9185	30.0647	-35.3015
24	5.809	1.0801	-1.8083	4.0202	1.7124	9.7304	-0.0384	-0.3796	0.9975	-0.0721	-0.032	-0.4128	-0.7367	0.8868	0.0704	0.555	-0.1387	-0.123	0.3603	-0.0982	0.7171	-2.4363	35.2066	-21.4623

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	0 - 65	1 - 66
2	X-RAY DIFFRACTION	2	A	A	66 - 103	67 - 104
3	X-RAY DIFFRACTION	3	A	A	104 - 125	105 - 126
4	X-RAY DIFFRACTION	4	A	A	126 - 179	127 - 180
5	X-RAY DIFFRACTION	5	B	B	0 - 65	1 - 66
6	X-RAY DIFFRACTION	6	B	B	66 - 103	67 - 104
7	X-RAY DIFFRACTION	7	B	B	104 - 125	105 - 126
8	X-RAY DIFFRACTION	8	B	B	126 - 179	127 - 180
9	X-RAY DIFFRACTION	9	C	C	0 - 65	1 - 66
10	X-RAY DIFFRACTION	10	C	C	66 - 103	67 - 104
11	X-RAY DIFFRACTION	11	C	C	104 - 125	105 - 126
12	X-RAY DIFFRACTION	12	C	C	126 - 179	127 - 180
13	X-RAY DIFFRACTION	13	D	D	0 - 65	1 - 66
14	X-RAY DIFFRACTION	14	D	D	66 - 103	67 - 104
15	X-RAY DIFFRACTION	15	D	D	104 - 125	105 - 126
16	X-RAY DIFFRACTION	16	D	D	126 - 179	127 - 180
17	X-RAY DIFFRACTION	17	E	E	0 - 65	1 - 66
18	X-RAY DIFFRACTION	18	E	E	66 - 103	67 - 104
19	X-RAY DIFFRACTION	19	E	E	104 - 125	105 - 126
20	X-RAY DIFFRACTION	20	E	E	126 - 179	127 - 180
21	X-RAY DIFFRACTION	21	F	F	0 - 65	1 - 66
22	X-RAY DIFFRACTION	22	F	F	66 - 103	67 - 104
23	X-RAY DIFFRACTION	23	F	F	104 - 125	105 - 126
24	X-RAY DIFFRACTION	24	F	F	126 - 179	127 - 180

Refinement

*PLUS

Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Num. reflection all: 37877 / Num. reflection obs: 36669 / R_factor R_free: 0.2855 / R_factor R_work: 0.2468

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.021
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	2.337
X-RAY DIFFRACTION	r_dihedral_angle_d
X-RAY DIFFRACTION	r_dihedral_angle_deg	21.101

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