PDB-2bei: X-ray structure of thialysine n-acetyltransferase (SSAT2) from ho...

ID or keywords:

Entry

Database: PDB / ID: 2bei

Title

X-ray structure of thialysine n-acetyltransferase (SSAT2) from homo sapiens

Components

Diamine acetyltransferase 2

Keywords

TRANSFERASE / SSAT2 / BC011751 / AAH11751 / THIALYSINE N-ACETYLTRANSFERASE /

STRUCTURAL GENOMICS /

PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG

Function / homology

Function and homology information

putrescine acetylation / nor-spermidine metabolic process / spermine acetylation / spermidine acetylation /

diamine N-acetyltransferase /

diamine N-acetyltransferase activity /

N-acetyltransferase activity /

Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / extracellular exosome / identical protein binding /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.842 Å

Authors

Wesenberg, G.E. / Phillips Jr., G.N. / Han, B.W. / Bitto, E. / Bingman, C.A. / Bae, E. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: Proteins / Year: 2006
Title: Crystal structure of Homo sapiens thialysine Nepsilon-acetyltransferase (HsSSAT2) in complex with acetyl coenzyme A.
Authors: Han, B.W. / Bingman, C.A. / Wesenberg, G.E. / Phillips, G.N.

History

Deposition	Oct 24, 2005	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 1, 2005	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Oct 18, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2bei.cif.gz	83.6 KB	Display	PDBx/mmCIF format
PDB format	pdb2bei.ent.gz	64.8 KB	Display	PDB format
PDBx/mmJSON format	2bei.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/be/2bei ftp://data.pdbj.org/pub/pdb/validation_reports/be/2bei	HTTPS FTP

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Related structure data

Similar structure data	2q4v-d 5f49-2 4yfj-d 2pdo-3 4evs-d 2q9k-1 3uy4-d 3c4a-d 3qse-1 3qss-1 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: GO.36731

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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: Diamine acetyltransferase 2

B: Diamine acetyltransferase 2

hetero molecules

39.3 kDa, 2 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)	54.583, 83.621, 87.548
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Diamine acetyltransferase 2 / Spermidine/spermine N(1)-acetyltransferase 2 / Polyamine N-acetyltransferase 2 / SSAT2 Mass: 19228.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SAT2, SSAT2 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q96F10, diamine N-acetyltransferase
#2: Chemical	ChemComp-ACO / ACETYL COENZYME A / Acetyl-CoA Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula*: C₂₃H₃₈N₇O₁₇P₃S
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.6 Å³/Da / Density % sol: 52.6 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10 MG/ML PROTEIN, 16.4% PEG 5K, 0.10 M MOPS, 0.15 M Potassium Glutamte, pH 7.0, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 0.97911, 0.96388

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR

Radiation

Monochromator: CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97911	1
2	0.96388	1

Reflection

D res low: 80 Å

Redundancy (%)	ID	Number	R_merge(I) obs	Χ²	D res high (Å)	% possible obs
6.8	1	34249	0.077	0.982	1.85	97
7	2	31730	0.065	1.087	1.9	98.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.99	80	99.8	1	0.055	1.084	7
3.16	3.99	100	1	0.052	1.006	7.3
2.76	3.16	100	1	0.077	1.028	7.4
2.51	2.76	100	1	0.105	1.158	7.4
2.33	2.51	100	1	0.14	1.024	7.4
2.19	2.33	100	1	0.185	1.014	7.3
2.08	2.19	100	1	0.248	0.93	7
1.99	2.08	98.6	1	0.306	0.822	6.3
1.92	1.99	92.2	1	0.388	0.774	5.4
1.85	1.92	78.5	1	0.459	0.69	4.3
4.09	80	99.8	2	0.043	1.065	7
3.25	4.09	100	2	0.041	0.986	7.3
2.84	3.25	100	2	0.063	1.065	7.4
2.58	2.84	100	2	0.087	1.071	7.4
2.39	2.58	100	2	0.114	1.104	7.4
2.25	2.39	100	2	0.155	1.13	7.4
2.14	2.25	100	2	0.204	1.162	7.4
2.05	2.14	99.6	2	0.263	1.088	7
1.97	2.05	95.3	2	0.348	1.153	6.3
1.9	1.97	86	2	0.422	1.046	5.4

Reflection

Resolution: 1.842→43.774 Å / Num. obs: 34249 / % possible obs: 97 % / Redundancy: 6.8 % / R_merge(I) obs: 0.077 / Χ²: 0.982 / Net I/σ(I): 10.833

Reflection shell

Resolution: 1.842→1.92 Å / % possible obs: 78.5 % / Redundancy: 4.3 % / R_merge(I) obs: 0.459 / Mean I/σ(I) obs: 2.377 / Num. measured obs: 2725 / Χ²: 0.69 / % possible all: 78.5

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Phasing

Phasing

Method:

MAD

Phasing MAD set

Highest resolution: 1.84 Å / Lowest resolution: 40.52 Å

ID	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	0	0	0	0	30431	3496
ISO_2	0.762	0.763	0.856	0.771	27970	3328
ANO_1	0.761	0	1.067	0	29651	0
ANO_2	0.85	0	0.943	0	27601	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	8.08-40.52	0	0	0	0	300	172
ISO_1	5.77-8.08	0	0	0	0	597	182
ISO_1	4.73-5.77	0	0	0	0	794	186
ISO_1	4.1-4.73	0	0	0	0	958	189
ISO_1	3.67-4.1	0	0	0	0	1090	175
ISO_1	3.35-3.67	0	0	0	0	1223	189
ISO_1	3.11-3.35	0	0	0	0	1336	179
ISO_1	2.91-3.11	0	0	0	0	1443	168
ISO_1	2.74-2.91	0	0	0	0	1531	163
ISO_1	2.6-2.74	0	0	0	0	1630	180
ISO_1	2.48-2.6	0	0	0	0	1716	176
ISO_1	2.38-2.48	0	0	0	0	1792	180
ISO_1	2.28-2.38	0	0	0	0	1900	196
ISO_1	2.2-2.28	0	0	0	0	1959	176
ISO_1	2.13-2.2	0	0	0	0	2049	188
ISO_1	2.06-2.13	0	0	0	0	2074	190
ISO_1	2-2.06	0	0	0	0	2150	172
ISO_1	1.94-2	0	0	0	0	2130	172
ISO_1	1.89-1.94	0	0	0	0	2056	146
ISO_1	1.84-1.89	0	0	0	0	1703	117
ANO_1	8.08-40.52	0.538	0	1.606	0	300	0
ANO_1	5.77-8.08	0.428	0	2.34	0	597	0
ANO_1	4.73-5.77	0.485	0	2.078	0	794	0
ANO_1	4.1-4.73	0.606	0	1.736	0	958	0
ANO_1	3.67-4.1	0.562	0	1.887	0	1090	0
ANO_1	3.35-3.67	0.568	0	1.775	0	1223	0
ANO_1	3.11-3.35	0.586	0	1.691	0	1336	0
ANO_1	2.91-3.11	0.622	0	1.567	0	1443	0
ANO_1	2.74-2.91	0.656	0	1.409	0	1531	0
ANO_1	2.6-2.74	0.7	0	1.239	0	1630	0
ANO_1	2.48-2.6	0.782	0	1.092	0	1716	0
ANO_1	2.38-2.48	0.816	0	0.924	0	1792	0
ANO_1	2.28-2.38	0.872	0	0.767	0	1900	0
ANO_1	2.2-2.28	0.922	0	0.635	0	1959	0
ANO_1	2.13-2.2	0.944	0	0.546	0	2049	0
ANO_1	2.06-2.13	0.959	0	0.493	0	2062	0
ANO_1	2-2.06	0.977	0	0.421	0	2095	0
ANO_1	1.94-2	0.99	0	0.414	0	2007	0
ANO_1	1.89-1.94	0.994	0	0.395	0	1818	0
ANO_1	1.84-1.89	1.002	0	0.388	0	1351	0
ISO_2	8.08-40.52	0.493	0.499	1.744	1.327	300	172
ISO_2	5.77-8.08	0.503	0.505	2.522	1.683	597	182
ISO_2	4.73-5.77	0.667	0.732	2.007	1.348	794	186
ISO_2	4.1-4.73	0.739	0.783	1.562	1.162	958	189
ISO_2	3.67-4.1	0.646	0.687	1.733	1.193	1090	175
ISO_2	3.35-3.67	0.639	0.623	1.679	1.082	1223	189
ISO_2	3.11-3.35	0.646	0.655	1.625	1.023	1336	179
ISO_2	2.91-3.11	0.68	0.806	1.439	0.995	1443	168
ISO_2	2.74-2.91	0.664	0.653	1.319	0.861	1531	163
ISO_2	2.6-2.74	0.704	0.726	1.085	0.653	1630	180
ISO_2	2.48-2.6	0.711	0.741	0.93	0.609	1716	176
ISO_2	2.38-2.48	0.744	0.785	0.762	0.534	1791	180
ISO_2	2.28-2.38	0.743	0.765	0.638	0.439	1900	196
ISO_2	2.2-2.28	0.766	0.884	0.519	0.331	1959	176
ISO_2	2.13-2.2	0.782	0.884	0.43	0.317	2049	188
ISO_2	2.06-2.13	0.81	1.022	0.366	0.248	2069	190
ISO_2	2-2.06	0.857	0.948	0.301	0.218	2100	168
ISO_2	1.94-2	0.844	0.987	0.262	0.191	1998	164
ISO_2	1.89-1.94	0.882	1.055	0.226	0.161	1486	107
ISO_2	1.84-1.89	0	0	0	0	0	0
ANO_2	8.08-40.52	0.539	0	2	0	300	0
ANO_2	5.77-8.08	0.437	0	2.91	0	597	0
ANO_2	4.73-5.77	0.496	0	2.507	0	794	0
ANO_2	4.1-4.73	0.651	0	2.015	0	958	0
ANO_2	3.67-4.1	0.623	0	2.109	0	1090	0
ANO_2	3.35-3.67	0.631	0	1.93	0	1223	0
ANO_2	3.11-3.35	0.66	0	1.737	0	1336	0
ANO_2	2.91-3.11	0.706	0	1.496	0	1443	0
ANO_2	2.74-2.91	0.743	0	1.36	0	1531	0
ANO_2	2.6-2.74	0.813	0	1.071	0	1630	0
ANO_2	2.48-2.6	0.862	0	0.916	0	1716	0
ANO_2	2.38-2.48	0.89	0	0.754	0	1791	0
ANO_2	2.28-2.38	0.917	0	0.637	0	1900	0
ANO_2	2.2-2.28	0.953	0	0.522	0	1959	0
ANO_2	2.13-2.2	0.967	0	0.419	0	2049	0
ANO_2	2.06-2.13	0.971	0	0.384	0	2046	0
ANO_2	2-2.06	0.981	0	0.336	0	2042	0
ANO_2	1.94-2	0.989	0	0.321	0	1856	0
ANO_2	1.89-1.94	0.989	0	0.29	0	1340	0
ANO_2	1.84-1.89	0	0	0	0	0	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	4.325	66.442	81.39	SE	22.57	1.31
2	0.037	12.289	38.46	SE	25.46	1.34
3	11.395	77.098	64.941	SE	35.56	1.43
4	13.276	5.551	2.484	SE	47.49	1.14

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 34191

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
7.92-100	52	0.903	513
6.21-7.92	43	0.933	518
5.27-6.21	40.3	0.95	616
4.66-5.27	40.8	0.958	700
4.22-4.66	43.7	0.953	777
3.89-4.22	44.4	0.947	841
3.62-3.89	47.1	0.949	906
3.41-3.62	46	0.94	959
3.22-3.41	44.2	0.927	1005
3.07-3.22	50.5	0.924	1093
2.93-3.07	50	0.912	1097
2.81-2.93	51.2	0.899	1167
2.71-2.81	53	0.906	1194
2.61-2.71	52.9	0.898	1260
2.53-2.61	56.2	0.896	1299
2.45-2.53	60.6	0.89	1313
2.38-2.45	61.3	0.881	1367
2.32-2.38	62.6	0.892	1409
2.26-2.32	67.1	0.878	1443
2.2-2.26	66.2	0.895	1481
2.15-2.2	68.4	0.882	1507
2.1-2.15	70.9	0.886	1545
2.06-2.1	75.4	0.884	1586
2.01-2.06	76.2	0.879	1578
1.97-2.01	78	0.862	1638
1.94-1.97	78.4	0.86	1547
1.9-1.94	80.3	0.84	1525
1.84-1.9	84.6	0.746	2307

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	refmac_5.2.0005	refinement
PDB_EXTRACT	1.7	data extraction
SOLOMON		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 1.842→43.774 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.934 / WR_factor R_free: 0.258 / WR_factor R_work: 0.209 / SU B: 2.886 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.14
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS,no electron density on chain A ASP48 - ASN49, strong electron density on chain B FOR THOSE RESIDUES, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2489	1719	5.027 %	RANDOM
R_work	0.2045	-	-	-
all	0.207	-	-	-
obs	0.207	34192	96.68 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 32.177 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.771 Å²	0 Å²	0 Å²
2-	-	-1.709 Å²	0 Å²
3-	-	-	-0.062 Å²

Refinement step

Cycle: LAST / Resolution: 1.842→43.774 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2524	0	51	305	2880

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	2628
X-RAY DIFFRACTION	r_angle_refined_deg	1.576	1.979	3540
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.958	5	312
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.086	23.333	126
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.46	15	454
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.152	15	20
X-RAY DIFFRACTION	r_chiral_restr	0.126	0.2	373
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1975
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	1266
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	1796
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.255	0.2	292
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.185	0.2	46
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.302	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	1.878	2	1619
X-RAY DIFFRACTION	r_mcangle_it	2.843	4	2456
X-RAY DIFFRACTION	r_scbond_it	4.884	6	1197
X-RAY DIFFRACTION	r_scangle_it	6.472	8	1083

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.842-1.89	0.294	91	0.255	1752	2580	71.434
1.89-1.942	0.306	84	0.227	2140	2514	88.465
1.942-1.998	0.276	111	0.207	2207	2436	95.156
1.998-2.059	0.238	122	0.201	2218	2363	99.027
2.059-2.127	0.244	125	0.202	2161	2287	99.956
2.127-2.202	0.271	107	0.199	2149	2256	100
2.202-2.285	0.23	114	0.194	2040	2154	100
2.285-2.378	0.249	106	0.2	1990	2096	100
2.378-2.483	0.243	98	0.204	1885	1983	100
2.483-2.604	0.267	99	0.21	1803	1902	100
2.604-2.745	0.288	98	0.219	1731	1829	100
2.745-2.911	0.296	91	0.221	1634	1725	100
2.911-3.111	0.291	87	0.21	1555	1642	100
3.111-3.36	0.251	77	0.195	1441	1518	100
3.36-3.679	0.269	87	0.185	1336	1423	100
3.679-4.112	0.198	71	0.18	1202	1273	100
4.112-4.744	0.211	54	0.18	1089	1143	100
4.744-5.802	0.215	46	0.209	937	983	100
5.802-8.167	0.231	30	0.259	752	782	100
8.167-60.523	0.23	21	0.236	451	477	98.952

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+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

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Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi