PDB-4q7a: Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetyla...

ID or keywords:

Entry

Database: PDB / ID: 4q7a

Title

Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetylase from Sphaerobacter thermophilus

Components

N-acetyl-ornithine/N-acetyl-lysine deacetylase

Keywords

HYDROLASE /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta fold / alpha-beta sandwich

Function / homology

Function and homology information

[amino group carrier protein]-lysine hydrolase / lysine biosynthetic process via aminoadipic acid / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / cobalt ion binding / zinc ion binding /

cytoplasm
Similarity search - Function

Biological species

Sphaerobacter thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.048 Å

Authors

Kim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal Structure of N-acetyl-ornithine/N-acetyl-lysine Deacetylase from Sphaerobacter thermophilus
Authors: Kim, Y. / Tesar, C. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Apr 24, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 2, 2014	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4q7a.cif.gz	541.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4q7a.ent.gz	464.3 KB	Display	PDB format
PDBx/mmJSON format	4q7a.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/q7/4q7a ftp://data.pdbj.org/pub/pdb/validation_reports/q7/4q7a	HTTPS FTP

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Related structure data

Similar structure data	6lrg-1 1ikw-2 6dcq-d 30217 6olp-d 30216 6o2a-d 5fuu-d 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: MCSG-APC100723

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (2)

Deposited unit

A: N-acetyl-ornithine/N-acetyl-lysine deacetylase

B: N-acetyl-ornithine/N-acetyl-lysine deacetylase

C: N-acetyl-ornithine/N-acetyl-lysine deacetylase

D: N-acetyl-ornithine/N-acetyl-lysine deacetylase

hetero molecules

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

1

A: N-acetyl-ornithine/N-acetyl-lysine deacetylase

B: N-acetyl-ornithine/N-acetyl-lysine deacetylase

C: N-acetyl-ornithine/N-acetyl-lysine deacetylase

D: N-acetyl-ornithine/N-acetyl-lysine deacetylase

hetero molecules

A: N-acetyl-ornithine/N-acetyl-lysine deacetylase

B: N-acetyl-ornithine/N-acetyl-lysine deacetylase

C: N-acetyl-ornithine/N-acetyl-lysine deacetylase

D: N-acetyl-ornithine/N-acetyl-lysine deacetylase

hetero molecules

defined by author&software
314 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.540, 119.540, 119.212
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	77
Space group name H-M	P4₂

#1: Protein	N-acetyl-ornithine/N-acetyl-lysine deacetylase Mass: 39103.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphaerobacter thermophilus (bacteria) / Strain: DSM 20745 / Gene: Sthe_0214 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold / References: UniProt: D1C6B5
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1068 / 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: 2.72 Å³/Da / Density % sol: 54.82 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.2 M litium sulfate, 0.1 M phosphate-citrate pH 4.2, 20 %(w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2013 / Details: mirrors
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection twin	Operator: h,-k,-l / Fraction: 0.5
Reflection	Resolution: 2.05→50 Å / Num. all: 105065 / Num. obs: 105065 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / B_iso Wilson estimate: 21.67 Å² / R_sym value: 0.052 / Net I/σ(I): 11.8
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 5166 / R_sym value: 0.562 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		data collection
HKL-3000		phasing
SHELXD		phasing
MLPHARE		phasing
DM		model building
RESOLVE		model building
Coot		model building
PHENIX	(phenix.refine: 1.9_1678)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing
RESOLVE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.048→48.78 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 18.61 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.171	5145	5.04 %	random
R_work	0.154	-	-	-
obs	0.156	102060	96.96 %	-
all	-	102060	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 28.3 Å²

Refinement step

Cycle: LAST / Resolution: 2.048→48.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10391	0	45	1068	11504

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	10712
X-RAY DIFFRACTION	f_angle_d	0.792	14645
X-RAY DIFFRACTION	f_dihedral_angle_d	12.679	3845
X-RAY DIFFRACTION	f_chiral_restr	0.051	1680
X-RAY DIFFRACTION	f_plane_restr	0.005	1931

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
2.0479-2.0832	0.2303	183	0.1981	3414	3597	65
2.0832-2.1211	0.2172	220	0.1954	4298	4518	82
2.1211-2.1619	0.2285	245	0.1952	4646	4891	89
2.1619-2.206	0.2134	258	0.1897	4799	5057	92
2.206-2.254	0.2168	253	0.1861	4924	5177	93
2.254-2.3064	0.211	244	0.181	4915	5159	94
2.3064-2.3641	0.2105	282	0.1772	4937	5219	94
2.3641-2.428	0.1936	264	0.1748	4965	5229	95
2.428-2.4995	0.1909	274	0.175	4953	5227	94
2.4995-2.5801	0.1955	258	0.1769	4981	5239	95
2.5801-2.6723	0.2092	270	0.1737	4985	5255	95
2.6723-2.7793	0.1977	263	0.1713	5010	5273	95
2.7793-2.9058	0.204	264	0.1695	4963	5227	95
2.9058-3.059	0.1803	256	0.1607	5002	5258	95
3.059-3.2506	0.1897	249	0.1539	5009	5258	95
3.2506-3.5015	0.1573	229	0.1463	5033	5262	96
3.5015-3.8537	0.146	265	0.1332	5034	5299	95
3.8537-4.4111	0.1214	269	0.1126	4976	5245	95
4.4111-5.5562	0.1266	273	0.1223	5012	5285	95
5.5562-48.7264	0.1745	286	0.1564	5082	5368	94

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	0.8578	0.018	0.334	1.2055	-0.4981	1.5027	0.1019	-0.0616	0.0301	-0.0274	-0.0717	0.1348	-0.059	-0.2064	-0.0019	0.1334	-0.0197	0.0113	0.1223	0.001	0.1035	-28.1818	40.5508	26.4667
2	1.1059	0.407	-0.2465	1.2765	-0.2562	0.7908	0.1252	-0.2109	-0.1072	0.0693	-0.1201	0.0641	-0.0506	0.0786	-0.0208	0.1378	-0.0015	0.0097	0.1254	0.0004	0.1237	10.4017	50.2257	21.6686
3	1.0653	0.4765	-0.0838	0.3154	-0.1523	0.152	0.176	-0.1806	-0.0743	0.0547	-0.1005	-0.1104	0.0448	0.1209	-0.0375	0.192	-0.0671	0.0139	0.163	0.0088	0.1395	-14.9745	37.9044	33.3036
4	1.0163	0.0816	-0.5509	0.7623	-0.013	1.3721	-0.036	-0.008	0.1396	-0.064	0.0436	0.0745	-0.1804	-0.0819	0.0228	0.1216	-0.0167	-0.0059	0.1443	0.0065	0.1061	19.3024	87.9931	-41.2349
5	1.072	0.1935	-0.2151	1.1438	-0.1622	0.9774	-0.0529	0.106	-0.0125	-0.1253	0.0564	-0.078	-0.0489	0.0245	-0.0044	0.1451	-0.0039	-0.009	0.1533	0.0151	0.1367	9.5611	49.0494	-36.3827
6	0.385	0.5131	-0.3125	0.574	-0.3354	0.1284	-0.1585	0.0471	0.0298	-0.2847	0.173	0.0309	0.1756	-0.0825	-0.028	0.2214	-0.0835	0.0324	0.2126	0.0149	0.1794	17.6524	69.61	-49.6947
7	0.9328	-0.2889	-0.2408	1.0809	0.1391	1.2815	-0.1781	-0.0279	-0.0968	-0.1107	0.1353	-0.0485	-0.0215	0.0493	-0.0207	0.1408	-0.0732	0.013	0.1787	0.0165	0.0971	26.6205	80.8322	-45.8893
8	1.13	-0.0932	0.4981	0.9589	0.0348	1.1138	-0.0117	-0.1811	-0.1261	0.1763	0.0695	0.1497	0.033	-0.3955	-0.0064	0.1756	0.0091	0.013	0.228	0.0399	0.1599	-11.0519	25.0351	-2.3224
9	0.6671	-0.1694	-0.1043	0.6564	0.0499	1.1813	0.0744	0.0074	-0.1034	0.0824	-0.1099	-0.0514	0.1152	0.0993	-0.0061	0.1717	0.0357	-0.0107	0.1431	0.0382	0.1263	2.5947	26.1613	-4.2612
10	1.4397	-0.093	0.1137	2.8074	-0.0051	1.2312	-0.024	0.0883	0.2966	-0.1065	-0.0993	-0.0677	-0.2866	0.168	-0.0096	0.1773	0.0335	-0.0206	0.1802	0.0393	0.1573	17.8165	56.2608	-22.3031
11	0.4773	-0.33	0.1797	0.89	-0.4539	0.6162	-0.0699	-0.0236	0.0017	0.0226	0.0548	-0.0497	-0.0297	0.0627	0.0287	0.1043	0.0457	0.0041	0.1822	0.0075	0.1236	16.0579	40.0796	-19.9688
12	0.9079	0.3337	0.1296	0.5593	0.0267	0.4259	0.1743	0.0305	-0.2816	0.0114	-0.1183	-0.0325	0.3191	0.1238	-0.0373	0.2318	0.0812	-0.0081	0.1967	0.0473	0.2222	5.3555	16.6436	-9.2966
13	0.9363	-0.3286	0.333	0.7527	-0.3583	0.8115	0.1669	0.2614	-0.467	-0.0519	-0.0652	0.0076	0.3841	0.0684	-0.0091	0.2347	-0.002	-0.0439	0.0977	0.0008	0.2441	-5.7033	16.4799	-9.3027
14	0.8958	0.0263	-0.2726	1.2002	0.4881	1.3148	0.0172	0.1033	0.0389	-0.1486	-0.0034	-0.0811	-0.1729	0.027	0.0009	0.1754	0.0201	0.0304	0.1704	0.024	0.146	34.4015	66.8529	-11.881
15	2.2162	-0.6789	0.1273	0.7567	-0.0312	0.8941	-0.0472	0.0253	-0.1571	0.0201	-0.0105	0.0436	0.2715	-0.0888	0.0386	0.222	0.0163	0.0298	0.0791	-0.0054	0.0863	15.2443	42.3321	8.5006
16	0.7389	0.161	-0.5168	0.7551	0.0149	0.5382	0.1771	0.1057	0.0629	-0.1221	-0.1408	-0.0752	0.0927	0.0196	0.0118	0.1914	0.0499	0.0397	0.1391	0.0298	0.1308	19.8563	47.0154	3.1876
17	0.7199	0.3067	-0.1792	0.9155	0.0025	0.4638	-0.0023	0.0076	-0.0699	0.0342	0.0241	-0.2182	0.0869	0.2183	-0.0259	0.1628	0.073	0.0118	0.2292	0.0243	0.161	36.987	50.7988	-4.1482
18	0.889	-0.3007	-0.5352	0.9387	0.2989	1.0438	-0.0653	-0.0847	0.0843	0.0866	0.1055	-0.3657	0.0325	0.2573	0.0004	0.1874	-0.0042	0.0233	0.2232	-0.0165	0.2189	41.3081	66.5401	-2.6437

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 163 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 164 through 257 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 258 through 361 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 163 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 164 through 257 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 258 through 313 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 314 through 361 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 10 through 123 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 124 through 165 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 166 through 185 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 186 through 265 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 266 through 313 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 314 through 361 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 9 through 165 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 166 through 209 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 210 through 249 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 250 through 313 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 314 through 353 )

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