PDB-4r9m: Crystal structure of spermidine N-acetyltransferase from Escheric...

ID or keywords:

Entry

Database: PDB / ID: 4r9m

Title

Crystal structure of spermidine N-acetyltransferase from Escherichia coli

Components

Spermidine N(1)-acetyltransferase

Keywords

TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / spermidine/spermine

Function / homology

Function and homology information

diamine N-acetyltransferase complex / polyamine catabolic process / spermine catabolic process / spermidine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / coenzyme A metabolic process / magnesium ion binding / protein-containing complex / identical protein binding
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 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: Acta Crystallogr D Struct Biol / Year: 2019
Title: Analysis of crystalline and solution states of ligand-free spermidine N-acetyltransferase (SpeG) from Escherichia coli.
Authors: Filippova, E.V. / Weigand, S. / Kiryukhina, O. / Wolfe, A.J. / Anderson, W.F.

History

Deposition	Sep 5, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Jun 26, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3	Sep 20, 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 / 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 / _struct_ref_seq_dif.details / _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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PDBx/mmCIF format	4r9m.cif.gz	224.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4r9m.ent.gz	182.3 KB	Display	PDB format
PDBx/mmJSON format	4r9m.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4r9m_validation.pdf.gz	457.2 KB	Display	wwPDB validaton report
Full document	4r9m_full_validation.pdf.gz	467.7 KB	Display
Data in XML	4r9m_validation.xml.gz	19.9 KB	Display
Data in CIF	4r9m_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r9/4r9m ftp://data.pdbj.org/pub/pdb/validation_reports/r9/4r9m	HTTPS FTP

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Related structure data

Related structure data	6cy6C 3eg7 PDB Unreleased entryS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ygo-1 6vfm-1 5wif-1 6cx8-1 6d72-1 4jly-1 7kwh-d 6cy6-1 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-idp91767

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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: Spermidine N(1)-acetyltransferase

B: Spermidine N(1)-acetyltransferase

C: Spermidine N(1)-acetyltransferase

hetero molecules

74 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Spermidine N(1)-acetyltransferase

B: Spermidine N(1)-acetyltransferase

C: Spermidine N(1)-acetyltransferase

hetero molecules

A: Spermidine N(1)-acetyltransferase

B: Spermidine N(1)-acetyltransferase

C: Spermidine N(1)-acetyltransferase

hetero molecules

A: Spermidine N(1)-acetyltransferase

B: Spermidine N(1)-acetyltransferase

C: Spermidine N(1)-acetyltransferase

hetero molecules

A: Spermidine N(1)-acetyltransferase

B: Spermidine N(1)-acetyltransferase

C: Spermidine N(1)-acetyltransferase

hetero molecules

defined by author&software
296 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	110.919, 110.919, 108.505
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-201- MG
2	1	A-304- HOH

#1: Protein	Spermidine N(1)-acetyltransferase / Diamine acetyltransferase / SAT Mass: 24663.969 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Gene: b1584, JW1576, speG / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: P0A951, diamine N-acetyltransferase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.26 Å³/Da / Density % sol: 45.46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 3 M Sodium Formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2011 / Details: Beryllium lenses
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.9→30 Å / Num. all: 15432 / Num. obs: 15432 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / R_merge(I) obs: 0.061 / Net I/σ(I): 32.3
Reflection shell	Resolution: 2.9→2.95 Å / Redundancy: 8 % / R_merge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHASER		phasing
REFMAC	5.7.0032	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EG7

3eg7
PDB Unreleased entry

Resolution: 2.9→29.61 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.913 / SU B: 34.52 / SU ML: 0.295 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2588	774	5 %	RANDOM
R_work	0.17574	-	-	-
obs	0.17967	14640	98.92 %	-
all	-	14640	-	-

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: 83.45 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	0 Å²	-0 Å²
2-	-	-0.05 Å²	0 Å²
3-	-	-	0.1 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→29.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4179	0	1	21	4201

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	4276
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.84	1.945	5752
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.277	5	490
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.379	23.306	242
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.46	15	772
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.553	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.135	0.2	598
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3289
X-RAY DIFFRACTION	r_gen_planes_other
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	4.871	6.165	1978
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	6.966	9.239	2462
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	6.56	6.618	2297
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined	11.2	52.356	6446
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.351	52	-
R_work	0.256	1066	-
obs	-	-	98.85 %

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	0.5979	-0.69	-3.0717	0.8327	3.6589	16.1972	-0.0897	-0.1221	0.1039	0.1002	0.1716	0.0205	0.5609	0.4968	-0.0819	0.4723	0.049	-0.0694	0.7946	0.0793	0.5644	16.5421	37.1958	21.2913
2	4.2616	-0.8776	0.521	1.7731	-0.0073	1.9417	0.1042	0.1485	-0.3034	-0.09	-0.2155	0.1403	0.1654	-0.0357	0.1113	0.088	-0.0212	0.0065	0.1948	0.006	0.0694	15.9575	16.2266	40.3678
3	2.4983	-0.2401	-0.3149	1.3159	0.2093	1.7156	0.1416	0.3595	0.2138	-0.1009	-0.099	-0.0872	-0.3102	0.0162	-0.0426	0.1314	-0.0325	0.0287	0.2115	0.0932	0.0672	21.5409	31.4279	39.5734
4	2.6344	-2.0448	-0.518	5.2747	0.4211	1.9514	0.1469	0.1942	0.6228	-0.0363	0.0533	-0.8895	-0.2696	0.2238	-0.2002	0.1511	-0.0869	0.0068	0.2094	0.0676	0.2157	30.5153	33.0455	46.2064
5	2.6251	-0.1531	-0.9342	0.238	-1.2207	8.7916	-0.3624	0.9023	0.1774	-0.0056	-0.0455	-0.0628	-0.0289	-0.0962	0.408	0.1943	-0.1104	-0.069	0.4226	0.071	0.0873	9.9475	-23.6636	32.5931
6	7.734	1.0423	-0.8617	0.8285	-1.7895	4.4789	0.424	0.3787	0.8146	0.1891	0.1782	0.3611	-0.2342	-0.2783	-0.6022	0.1476	0.0722	0.0886	0.1778	0.0684	0.2597	2.8016	-20.7773	43.8451
7	3.2333	-0.4255	0.7894	1.3185	-1.0722	4.5249	-0.1272	0.4133	0.0669	-0.0037	-0.0168	-0.1758	-0.1193	0.2302	0.144	0.1436	0.0778	-0.0139	0.1523	-0.0152	0.0289	15.862	-26.3425	41.6202
8	2.8748	0.3369	-0.9471	1.4959	-0.2338	1.3903	-0.1067	0.5836	-0.4429	-0.1125	0.0024	-0.0816	0.3398	0.0996	0.1043	0.1941	0.0634	0.0171	0.2141	-0.1175	0.0932	17.0213	-37.8205	39.5455
9	5.0781	1.1813	-0.2686	1.314	-0.378	0.6638	0.0244	0.3511	-1.2691	-0.0708	0.0365	-0.1752	0.262	0.1024	-0.0609	0.2455	0.1009	-0.0287	0.1489	-0.1032	0.3508	11.6708	-42.1636	47.133
10	0.9596	-1.1222	1.1642	1.4422	-0.8573	3.3992	0.2428	0.0972	-0.1484	-0.4522	-0.1447	0.2011	-0.2101	0.0497	-0.0981	0.3345	-0.0474	-0.0873	0.2582	0.0042	0.0669	25.2608	-2.0969	32.0002
11	0.2842	0.8531	1.1211	6.9575	0.4976	6.3153	0.0367	-0.0055	-0.0175	-0.5313	0.4426	0.568	0.6031	-0.2558	-0.4793	0.1533	0.0309	-0.09	0.2361	0.0543	0.1375	20.6225	-11.0176	42.5639
12	0.7536	0.0492	0.6551	5.4963	-2.1585	1.5335	-0.125	0.0525	0.1875	-0.3792	0.0119	0.2929	0.1287	0.038	0.1131	0.1508	0.033	0.0089	0.2199	-0.0282	0.1182	26.9479	-0.5057	39.5998
13	1.2533	0.2477	-0.2492	2.7126	-0.2807	1.1327	-0.1368	0.2053	-0.0453	-0.3135	0.0328	-0.3942	0.064	0.3664	0.1039	0.1047	0.0487	0.0359	0.2649	0.0003	0.0718	40.6576	-3.4793	41.2672
14	1.669	0.8711	0.5502	5.0076	-0.5492	0.9073	0.1046	0.2634	-0.2427	-0.1768	-0.1064	-0.8614	0.1252	0.2531	0.0018	0.0728	0.0716	0.0188	0.2362	-0.0407	0.166	42.4241	-11.075	47.4008

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 8
2	X-RAY DIFFRACTION	2	A	9 - 61
3	X-RAY DIFFRACTION	3	A	62 - 134
4	X-RAY DIFFRACTION	4	A	135 - 172
5	X-RAY DIFFRACTION	5	B	5 - 30
6	X-RAY DIFFRACTION	6	B	31 - 53
7	X-RAY DIFFRACTION	7	B	54 - 82
8	X-RAY DIFFRACTION	8	B	83 - 142
9	X-RAY DIFFRACTION	9	B	143 - 172
10	X-RAY DIFFRACTION	10	C	5 - 23
11	X-RAY DIFFRACTION	11	C	24 - 48
12	X-RAY DIFFRACTION	12	C	49 - 76
13	X-RAY DIFFRACTION	13	C	77 - 142
14	X-RAY DIFFRACTION	14	C	143 - 172

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