PDB-3kzl: Crystal structure of BA2930 mutant (H183G) in complex with AcCoA

ID or keywords:

Entry

Database: PDB / ID: 3kzl

Title

Crystal structure of BA2930 mutant (H183G) in complex with AcCoA

Components

Aminoglycoside N3-acetyltransferase

Keywords

TRANSFERASE / putative AMINOGLYCOSIDE N3-ACETYLTRANSFERASE / AcCoA / Acyltransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside 3-N-acetyltransferase / Aminoglycoside 3-N-acetyltransferase-like / response to antibiotic / ACETYL COENZYME *A / Aminoglycoside N(3)-acetyltransferase / Aminoglycoside N(3)-acetyltransferase

Function and homology information

Biological species

Bacillus anthracis (anthrax bacterium)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Klimecka, M.M. / Chruszcz, M. / Porebski, P.J. / Cymborowski, M. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Structural Analysis of a Putative Aminoglycoside N-Acetyltransferase from Bacillus anthracis.
Authors: Klimecka, M.M. / Chruszcz, M. / Font, J. / Skarina, T. / Shumilin, I. / Onopryienko, O. / Porebski, P.J. / Cymborowski, M. / Zimmerman, M.D. / Hasseman, J. / Glomski, I.J. / Lebioda, L. / ...

History

Deposition	Dec 8, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 22, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 3, 2011	Group: Database references
Revision 1.3	Oct 13, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Apr 13, 2022	Group: Database references / Structure summary / Category: audit_author / citation_author Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3kzl.cif.gz	225.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3kzl.ent.gz	191.6 KB	Display	PDB format
PDBx/mmJSON format	3kzl.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3kzl_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3kzl_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3kzl_validation.xml.gz	44.1 KB	Display
Data in CIF	3kzl_validation.cif.gz	62.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kz/3kzl ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kzl	HTTPS FTP

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Related structure data

Related structure data	3e4fC 3ijwC 3n0mC 3n0sC C: citing same article (ref.)
Similar structure data	3slb-1 3slf-d 3n0m-d 3ijw-d 6qz2-9 6qga-1 3n0s-1 6qz4-2 6jtu-3 6qgb-1 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	TargetDB: IDP00044

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Aminoglycoside N3-acetyltransferase

D: Aminoglycoside N3-acetyltransferase

C: Aminoglycoside N3-acetyltransferase

B: Aminoglycoside N3-acetyltransferase

hetero molecules

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

1

A: Aminoglycoside N3-acetyltransferase

B: Aminoglycoside N3-acetyltransferase

hetero molecules

defined by author&software
62.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Aminoglycoside N3-acetyltransferase

C: Aminoglycoside N3-acetyltransferase

hetero molecules

defined by author&software
62.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.831, 109.182, 73.721
Angle α, β, γ (deg.)	90.00, 111.91, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ADCB

#1: Protein	Aminoglycoside N3-acetyltransferase Mass: 30256.074 Da / Num. of mol.: 4 / Mutation: H183G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: aacC7, BA_2930, GBAA2930, GBAA_2930, GBAA_2930; / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3) / References: UniProt: Q81P86, UniProt: A0A1J9VPY4*PLUS

#1: Protein

Aminoglycoside N3-acetyltransferase

Mass: 30256.074 Da / Num. of mol.: 4 / Mutation: H183G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: aacC7, BA_2930, GBAA2930, GBAA_2930, GBAA_2930; / Plasmid: pMCSG7 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3) / References: UniProt: Q81P86, UniProt: A0A1J9VPY4*PLUS

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Non-polymers , 5 types, 473 molecules

#2: Chemical	ChemComp-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula*: C₂₃H₃₈N₇O₁₇P₃S
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 455 / 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: 44.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Hepes, pH 7.5, 0.2 M MgCl2, 15% PEG 3350, 1% CHAPSO, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 16, 2009 / Details: mirrors
Radiation	Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. all: 61626 / Num. obs: 61626 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / R_merge(I) obs: 0.117 / R_sym value: 0.117 / Net I/σ(I): 16.7
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.571 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2718 / R_sym value: 0.571 / % possible all: 87.8

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
HKL-3000		phasing
SHELXD		phasing
SHELXE		model building
MLPHARE		phasing
DM		model building
SOLVE		phasing
RESOLVE		model building
ARP/wARP		model building
REFMAC	5.5.0072	refinement
Coot		model building
HKL-2000		data reduction
HKL-2000		data scaling
DM		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→34.57 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.926 / SU B: 10.617 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.244 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23181	3081	5.1 %	RANDOM
R_work	0.17997	-	-	-
obs	0.18255	57645	98.76 %	-
all	-	57645	-	-

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: 14.302 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.08 Å²	0 Å²	-0.82 Å²
2-	-	0.4 Å²	0 Å²
3-	-	-	-0.93 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→34.57 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8143	0	232	455	8830

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	8579
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.02	5699
X-RAY DIFFRACTION	r_angle_refined_deg	1.516	1.98	11689
X-RAY DIFFRACTION	r_angle_other_deg	0.917	3	13932
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.028	5	1064
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.936	24.099	344
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.368	15	1399
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.346	15	51
X-RAY DIFFRACTION	r_chiral_restr	0.193	0.2	1315
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	9410
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1677
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	0.715	1.5	5293
X-RAY DIFFRACTION	r_mcbond_other	0.168	1.5	2161
X-RAY DIFFRACTION	r_mcangle_it	1.354	2	8567
X-RAY DIFFRACTION	r_scbond_it	2.562	3	3286
X-RAY DIFFRACTION	r_scangle_it	3.823	4.5	3121
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.261	208	-
R_work	0.229	3874	-
obs	-	-	90.97 %

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	1.1091	-0.0777	0.3229	1.2925	0.1577	0.5918	-0.068	0.0066	0.1955	0.0979	0.034	-0.0196	-0.1216	-0.0073	0.034	0.0746	-0.0039	-0.0051	0.067	-0.0023	0.0443	5.848	16.4474	41.1306
2	1.128	0.038	0.2372	1.5496	0.3745	0.8972	-0.0282	0.041	0.0208	-0.0125	0.0055	0.2358	-0.0431	-0.1156	0.0228	0.0279	-0.0144	-0.008	0.0887	0.0115	0.0556	-5.3666	6.6886	36.6763
3	1.5078	0.355	0.4071	1.8933	0.4981	0.7877	-0.1384	0.2368	0.1634	-0.292	0.026	0.4092	-0.1566	-0.1368	0.1124	0.0958	-0.0041	-0.0613	0.1417	0.034	0.0977	-9.3212	11.175	29.5612
4	0.79	-0.284	0.2891	1.0839	0.015	0.8012	-0.0064	0.0769	-0.0984	-0.042	0.0162	0.0886	0.0419	0.0047	-0.0099	0.0399	0.0025	0.014	0.0612	0.0003	0.0222	13.8784	-8.7823	35.6378
5	0.789	-0.3595	0.2706	1.316	0.2116	0.8521	-0.0807	-0.0779	0.0343	0.1498	0.0461	-0.0609	-0.0277	0.0019	0.0346	0.0553	0.0055	-0.0025	0.059	0.0077	0.009	20.7582	-2.9424	48.6388
6	5.3278	-1.1605	-0.2204	2.8991	0.9349	4.0381	-0.4002	-0.3764	0.3067	0.3205	0.2486	-0.3435	-0.2856	0.1941	0.1516	0.122	-0.0016	-0.0831	0.0726	-0.0213	0.067	27.941	5.959	55.7263
7	3.2379	-0.7079	1.0244	0.9925	0.51	1.0992	0.066	0.3162	0.1025	0.0426	-0.008	-0.2058	0.1857	0.2628	-0.058	0.1186	0.074	0.0541	0.1451	0.0546	0.0927	31.4487	-15.3774	37.3906
8	1.2007	0.693	0.4312	1.6172	0.3546	0.6881	-0.0356	0.0994	0.0386	0.1451	0.0879	-0.0194	-0.048	0.0841	-0.0523	0.0759	-0.0009	0.0085	0.079	-0.0015	0.0119	19.6354	17.5083	6.0153
9	0.9266	0.0057	-0.1172	2.2082	0.6476	0.6911	-0.0318	0.0557	-0.0293	0.1022	0.01	0.3105	0.0359	-0.0904	0.0218	0.0448	-0.0131	0.0161	0.0845	0.0086	0.0558	8.4325	6.9273	2.4173
10	1.9113	0.3623	0.227	3.2178	0.168	0.9117	-0.1063	0.2805	0.0412	-0.3608	-0.021	0.66	-0.0834	-0.1383	0.1272	0.0533	0.0111	-0.076	0.1116	-0.0207	0.1478	4.5461	11.3276	-5.1489
11	1.5409	-0.1579	1.04	2.2629	0.1473	1.5239	-0.2361	-0.0268	0.4988	-0.1859	0.0084	0.5549	-0.3266	-0.0851	0.2278	0.1372	0.0087	-0.0853	0.0608	0.0137	0.3644	4.552	25.2183	-2.8151
12	0.9626	-0.3339	0.3197	0.8009	0.0336	0.8844	-0.0892	0.0998	-0.084	0.009	0.0529	0.0381	0.086	0.0524	0.0363	0.0677	-0.0002	0.0342	0.0919	0.0075	0.0212	27.894	-8.5976	2.7013
13	0.9673	-0.1921	0.1756	0.9134	0.2404	0.5562	-0.1284	-0.0792	0.0435	0.1517	0.0951	-0.0799	0.0062	0.075	0.0334	0.108	0.0231	-0.0078	0.0911	0.0096	0.0164	34.8793	-1.2981	14.82
14	3.6457	-0.2946	-0.4844	1.9111	0.0257	2.0827	-0.2735	-0.228	0.0834	0.204	0.2139	-0.3223	-0.0767	0.169	0.0596	0.1105	0.0194	-0.0644	0.1152	-0.0522	0.0739	42.1022	7.9657	20.4056
15	2.172	-0.1813	0.4707	1.0806	0.4649	0.6956	-0.0763	0.1527	-0.0722	0.0207	0.0616	-0.16	0.0603	0.2217	0.0148	0.1032	0.0186	0.026	0.1199	0.0029	0.0815	46.0861	-14.6461	4.592
16	3.4435	0.7913	1.0078	1.9765	-0.2935	1.574	-0.1083	0.1249	0.6149	-0.1633	0.0715	0.5025	-0.2271	-0.2185	0.0368	0.1423	0.0178	-0.0936	0.0982	0.0669	0.2678	-9.6306	25.3586	33.079

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 83
2	X-RAY DIFFRACTION	2	A	84 - 185
3	X-RAY DIFFRACTION	3	A	186 - 241
4	X-RAY DIFFRACTION	4	B	-1 - 83
5	X-RAY DIFFRACTION	5	B	84 - 189
6	X-RAY DIFFRACTION	6	B	190 - 218
7	X-RAY DIFFRACTION	7	B	219 - 263
8	X-RAY DIFFRACTION	8	C	0 - 83
9	X-RAY DIFFRACTION	9	C	84 - 185
10	X-RAY DIFFRACTION	10	C	186 - 241
11	X-RAY DIFFRACTION	11	C	242 - 262
12	X-RAY DIFFRACTION	12	D	-1 - 83
13	X-RAY DIFFRACTION	13	D	84 - 189
14	X-RAY DIFFRACTION	14	D	190 - 219
15	X-RAY DIFFRACTION	15	D	220 - 263
16	X-RAY DIFFRACTION	16	A	242 - 262

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