PDB-5isv: Crystal structure of the ribosomal-protein-S18-alanine N-acetyltr...

ID or keywords:

Entry

Database: PDB / ID: 5isv

Title

Crystal structure of the ribosomal-protein-S18-alanine N-acetyltransferase from Escherichia coli

Components

Ribosomal-protein-alanine acetyltransferase

Keywords

TRANSFERASE / RimI / AcCoA / GNAT / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

[ribosomal protein bS18]-alanine N-acetyltransferase / protein-N-terminal-alanine acetyltransferase activity / N-acetyltransferase activity / protein-lysine-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / protein modification process / cytoplasm
Similarity search - Function

Biological species

Escherichia coli O157:H7 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 Å

Authors

Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Grimshaw, S. / Wolfe, A.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: Crystal structure of the ribosomal-protein-S18-alanine N-acetyltransferase from Escherichia coli
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Grimshaw, S. / Wolfe, A.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Mar 15, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 13, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5isv.cif.gz	157.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5isv.ent.gz	126.6 KB	Display	PDB format
PDBx/mmJSON format	5isv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5isv_validation.pdf.gz	431 KB	Display	wwPDB validaton report
Full document	5isv_full_validation.pdf.gz	432.8 KB	Display
Data in XML	5isv_validation.xml.gz	16.9 KB	Display
Data in CIF	5isv_validation.cif.gz	25.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/is/5isv ftp://data.pdbj.org/pub/pdb/validation_reports/is/5isv	HTTPS FTP

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Related structure data

Related structure data	2cntS S: Starting model for refinement
Similar structure data	1zkc-2 2ful-4 2anb-d 3hdc-d 2r1b-1 2ful-3 2r1b-2 2pso-3 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-idp92642

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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: Ribosomal-protein-alanine acetyltransferase

B: Ribosomal-protein-alanine acetyltransferase

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

1

A: Ribosomal-protein-alanine acetyltransferase

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

2

B: Ribosomal-protein-alanine acetyltransferase

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

Unit cell

Length a, b, c (Å)	40.222, 41.785, 46.404
Angle α, β, γ (deg.)	93.74, 90.08, 116.52
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASN	ASN	ASN	ASN	A	A	2 - 128	2 - 128
2	1	ASN	ASN	ASN	ASN	B	B	2 - 128	2 - 128
1	2	GLU	GLU	ILE	ILE	A	A	137 - 146	137 - 146
2	2	GLU	GLU	ILE	ILE	B	B	137 - 146	137 - 146

NCS oper:

ID	Code	Matrix	Vector
1	given	(1), (1), (1)
2	given	(-0.999901, -0.013934, -0.001825), (0.014051, -0.989203, -0.145879), (0.000227, -0.14589, 0.989301)	67.22107, 105.12492, 31.04638

#1: Protein	Ribosomal-protein-alanine acetyltransferase / Acetylating enzyme for N-terminal of ribosomal protein S18 Mass: 18591.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: rimI, Z5974, ECs5331 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic References: UniProt: P0A946, UniProt: P0A944*PLUS, ribosomal-protein-alanine N-acetyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Ribosomal-protein-alanine acetyltransferase / Acetylating enzyme for N-terminal of ribosomal protein S18

Mass: 18591.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli O157:H7 (bacteria) / Gene: rimI, Z5974, ECs5331 / Plasmid: pMCSG28 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic
References: UniProt: P0A946, UniProt: P0A944*PLUS, ribosomal-protein-alanine N-acetyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 322 / 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: 1.87 Å³/Da / Density % sol: 34.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.01 M tri-sodium citrate, 33% (w/v) PEG6000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2016 / Details: beryllium lenses
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 1.35→30 Å / Num. obs: 56272 / % possible obs: 95 % / Redundancy: 3.9 % / R_merge(I) obs: 0.045 / Net I/σ(I): 38.05
Reflection shell	Resolution: 1.35→1.37 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.335 / Mean I/σ(I) obs: 3.3 / % possible all: 90

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2CNT

2cnt

Resolution: 1.35→30 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.962 / SU B: 3.731 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20902	2899	5.2 %	RANDOM
R_work	0.15571	-	-	-
obs	0.15837	53373	94.83 %	-

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: 28.192 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.38 Å²	1.85 Å²	-1.03 Å²
2-	-	0.02 Å²	-0.36 Å²
3-	-	-	-2.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.35→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2463	0	0	323	2786

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	2658
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2469
X-RAY DIFFRACTION	r_angle_refined_deg	1.662	1.942	3635
X-RAY DIFFRACTION	r_angle_other_deg	1.178	3	5661
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.696	5	341
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.529	24.307	137
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.122	15	435
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.716	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.108	0.2	401
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3173
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	659
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	1.948	1.675	1322
X-RAY DIFFRACTION	r_mcbond_other	1.946	1.674	1321
X-RAY DIFFRACTION	r_mcangle_it	2.408	2.523	1677
X-RAY DIFFRACTION	r_mcangle_other	2.407	2.523	1678
X-RAY DIFFRACTION	r_scbond_it	2.582	2.014	1336
X-RAY DIFFRACTION	r_scbond_other	2.584	2.013	1337
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.103	2.913	1959
X-RAY DIFFRACTION	r_long_range_B_refined	4.557	16.479	3167
X-RAY DIFFRACTION	r_long_range_B_other	3.952	15.222	3018
X-RAY DIFFRACTION	r_rigid_bond_restr	2.182	3	5127
X-RAY DIFFRACTION	r_sphericity_free	36.421	5	101
X-RAY DIFFRACTION	r_sphericity_bonded	12.814	5	5294

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1950 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Type	Rms dev position (Å)	Weight position
A	loose positional	0.42	5
B	loose thermal	3.84	10

LS refinement shell

Resolution: 1.349→1.384 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	170	-
R_work	0.22	3746	-
obs	-	-	89.35 %

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	1.7722	0.2132	0.3523	0.8344	-0.0891	2.5316	-0.1095	0.1543	-0.2086	-0.1634	-0.0249	-0.0198	0.1425	-0.0218	0.1344	0.0865	-0.0454	0.0407	0.0596	-0.0259	0.0859	22.1784	45.1608	-11.1051
2	1.2542	0.2997	0.1249	0.6805	0.1228	1.4196	-0.0437	0.1025	0.0257	0.0119	0.0526	-0.0121	0.0838	0.0285	-0.0089	0.054	-0.0481	0.0252	0.0616	-0.0083	0.0744	23.8763	47.4954	-5.221
3	5.9561	-0.8382	0.9333	0.7925	0.0564	0.201	0.0135	-0.0306	-0.0698	0.1441	0.0034	0.0038	0.0511	-0.016	-0.017	0.0748	-0.0453	0.0092	0.0537	0.0048	0.0406	21.1771	46.1727	2.7286
4	2.0554	-1.8257	1.4907	2.7053	-1.3518	2.214	-0.0004	-0.1563	0.034	0.0459	0.1419	-0.0225	-0.1045	-0.1341	-0.1416	0.0576	-0.0479	0.0297	0.0708	-0.0016	0.0658	23.5582	58.3345	1.5369
5	1.7396	-0.7178	0.2986	3.4519	-2.0293	3.0256	-0.0141	0.0895	0.183	-0.007	-0.0285	-0.1154	-0.184	0.021	0.0425	0.0482	-0.0287	0.0236	0.0327	-0.0051	0.0643	24.7896	67.116	-5.857
6	2.3627	-1.2622	2.0552	0.9172	-1.595	2.8222	-0.0462	0.0002	0.1135	-0.0121	-0.0181	-0.0616	0.0109	0.0542	0.0643	0.0662	-0.0515	0.0346	0.0525	-0.0214	0.0906	35.4771	57.1677	6.7812
7	2.7029	-0.0305	-2.0501	3.3901	0.7017	2.1523	0.0275	0.1545	0.3345	-0.2755	-0.0027	-0.0253	-0.141	0.1152	-0.0248	0.0842	-0.0741	0.0159	0.1624	0.098	0.1991	47.5986	68.5497	-32.4235
8	2.3288	-1.3369	-1.472	1.9451	0.7561	3.6895	-0.0186	0.1919	0.0045	-0.1529	-0.0555	0.0072	-0.052	-0.1507	0.0741	0.0634	-0.0438	0.0106	0.0589	0.0074	0.0613	39.723	62.1833	-36.4514
9	3.5559	0.0426	0.2452	1.0904	-0.2282	1.3705	-0.0232	0.1175	0.1731	0.0549	0.0349	-0.0066	-0.0597	0.0278	-0.0117	0.0362	-0.0291	0.0182	0.0351	-0.0029	0.0511	42.949	64.0478	-27.0008
10	3.8637	0.5652	-0.4651	1.0493	-0.0396	0.8746	0.0649	-0.045	-0.0945	0.2397	-0.0291	-0.0412	-0.1161	0.0866	-0.0358	0.1086	-0.0592	0.0076	0.063	0.0027	0.0468	43.0727	61.7342	-19.5664
11	2.7786	-1.4885	0.4012	1.8586	0.6373	4.9259	0.0801	-0.0008	-0.2442	-0.0955	0.0007	0.1715	0.3735	0.1428	-0.0807	0.0747	-0.0111	-0.0053	0.0288	-0.002	0.0528	43.396	46.9214	-25.6501
12	3.1381	-1.0283	-2.7826	0.4294	1.0975	3.3558	-0.0117	-0.009	-0.1724	-0.0026	-0.0006	0.0445	0.0262	0.0191	0.0123	0.0545	-0.0289	0.0147	0.0243	-0.0008	0.0756	33.7957	50.5349	-19.7625

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 46
2	X-RAY DIFFRACTION	2	A	47 - 73
3	X-RAY DIFFRACTION	3	A	74 - 96
4	X-RAY DIFFRACTION	4	A	97 - 119
5	X-RAY DIFFRACTION	5	A	120 - 135
6	X-RAY DIFFRACTION	6	A	136 - 155
7	X-RAY DIFFRACTION	7	B	2 - 22
8	X-RAY DIFFRACTION	8	B	23 - 41
9	X-RAY DIFFRACTION	9	B	42 - 73
10	X-RAY DIFFRACTION	10	B	74 - 101
11	X-RAY DIFFRACTION	11	B	102 - 131
12	X-RAY DIFFRACTION	12	B	132 - 155

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