PDB-3pnt: Crystal Structure of the Streptococcus pyogenes NAD+ glycohydrola...

ID or keywords:

Entry

Database: PDB / ID: 3pnt

Title

Crystal Structure of the Streptococcus pyogenes NAD+ glycohydrolase SPN in complex with IFS, the Immunity Factor for SPN

Components

Immunity factor for SPN
NAD+-glycohydrolase

Keywords

HYDROLASE/HYDROLASE INHIBITOR / glycohydrolase /

NAD+ /

virulence factor / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

hydrolase activity
Similarity search - Function

Biological species

Streptococcus pyogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.8 Å

Authors

Smith, C.L. / Stine Elam, J. / Ellenberger, T. / Ghosh, J. / Pinkner, J.S. / Hultgren, S.J. / Caparon, M.G.

Citation

Journal: Structure / Year: 2011
Title: Structural Basis of Streptococcus pyogenes Immunity to Its NAD(+) Glycohydrolase Toxin.
Authors: Smith, C.L. / Ghosh, J. / Elam, J.S. / Pinkner, J.S. / Hultgren, S.J. / Caparon, M.G. / Ellenberger, T.

History

Deposition	Nov 19, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3pnt.cif.gz	173.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3pnt.ent.gz	148.2 KB	Display	PDB format
PDBx/mmJSON format	3pnt.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/pn/3pnt ftp://data.pdbj.org/pub/pdb/validation_reports/pn/3pnt	HTTPS FTP

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Related structure data

Related structure data	3qb2C C: citing same article (ref.)
Similar structure data	1pji-d 4kt6-1 3pns-5 2xzu-d 4kt6-2 1q2s-1 6rnr-d 6ro2-d 3zlg-2 5g1z-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NAD+-glycohydrolase

B: Immunity factor for SPN

C: NAD+-glycohydrolase

D: Immunity factor for SPN

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

1

A: NAD+-glycohydrolase

B: Immunity factor for SPN

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

2

C: NAD+-glycohydrolase

D: Immunity factor for SPN

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

Unit cell

Length a, b, c (Å)	198.817, 57.892, 89.699
Angle α, β, γ (deg.)	90.00, 107.20, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
1	2	B
2	2	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	6	A	197 - 445
2	1	1	6	C	197 - 445
1	1	2	6	B	2 - 161
2	1	2	6	D	2 - 161

NCS ensembles :

ID
1
2

#1: Protein	NAD+-glycohydrolase Mass: 31166.047 Da / Num. of mol.: 2 / Fragment: UNP residues 191-451 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: spn / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D7S065, NAD+ glycohydrolase
#2: Protein	Immunity factor for SPN / SPN immunity factor Mass: 19211.662 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: ifs / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2VJ58
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.57 Å³/Da / Density % sol: 52.2 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 8000, NaCl, Tris (8.0), vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 4.2.2 / Wavelength: 0.97892, 0.97938, 0.99510

Detector

Type: NOIR-1 / Detector: CCD

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97892	1
2	0.97938	1
3	0.9951	1

Reflection

Resolution: 2.8→42.72 Å / Num. all: 24375 / Num. obs: 24309

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Processing

Software

Name	Version	Classification	NB
REFMAC	5.5.0093	refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 2.8→42.72 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.893 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 38.308 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27811	1240	5.1 %	RANDOM
R_work	0.20802	-	-	-
obs	0.21166	23069	99.73 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 17.832 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.01 Å²	0 Å²	-0.03 Å²
2-	-	-0.08 Å²	0 Å²
3-	-	-	0.08 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→42.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6640	0	0	153	6793

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	6764
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4690
X-RAY DIFFRACTION	r_angle_refined_deg	1.193	1.967	9088
X-RAY DIFFRACTION	r_angle_other_deg	0.827	3	11473
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.453	5	817
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.996	25.092	326
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.322	15	1299
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.413	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.066	0.2	975
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	7449
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1335
X-RAY DIFFRACTION	r_mcbond_it	0.328	1.5	4079
X-RAY DIFFRACTION	r_mcbond_other	0.049	1.5	1664
X-RAY DIFFRACTION	r_mcangle_it	0.652	2	6560
X-RAY DIFFRACTION	r_scbond_it	1.081	3	2685
X-RAY DIFFRACTION	r_scangle_it	1.746	4.5	2528

Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	3424	LOOSE POSITIONAL	0.55	5
1	A	3424	LOOSE THERMAL	1.94	10
2	B	2221	LOOSE POSITIONAL	0.52	5
2	B	2221	LOOSE THERMAL	1.78	10

LS refinement shell

Resolution: 2.8→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.402	91	-
R_work	0.366	1700	-
obs	-	-	99.39 %

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	18.5362	6.5169	10.9874	5.9747	0.5088	9.5833	0.4683	-0.5092	0.4156	-0.4439	-0.9814	-0.1817	0.9431	0.4289	0.5131	0.4089	0.2904	0.1379	0.2862	0.0629	0.1946	85.7945	18.3362	79.6872
2	2.0697	-0.257	0.6144	1.8066	-0.8864	0.726	-0.1093	-0.3859	0.153	0.1675	0.0324	-0.0442	-0.2165	0.0332	0.0769	0.2207	0.0699	0.0206	0.3329	-0.0018	0.1121	84.9309	32.8047	75.2727
3	2.3562	0.698	0.1504	1.3507	0.3618	1.5186	-0.0517	0.0431	0.2212	-0.0839	0.011	0.012	-0.1178	0.089	0.0407	0.2745	0.0911	-0.0171	0.1606	-0.0023	0.2184	71.3315	37.4697	61.5607
4	1.8616	-0.4497	-0.1127	1.9345	0.0263	2.0026	-0.1495	-0.061	0.2028	-0.1365	0.0802	-0.1047	-0.1238	0.2821	0.0693	0.169	0.0229	-0.0105	0.1616	-0.0189	0.202	79.585	38.0803	63.8908
5	1.0267	-0.3181	-1.3325	1.4335	0.6726	2.0666	0.0197	0.178	0.1482	-0.2317	-0.0664	0.2059	-0.3254	-0.2835	0.0468	0.3365	0.0784	-0.1302	0.0587	0.0125	0.2791	70.3813	43.2916	59.2937
6	0.3687	0.2484	0.9988	4.7425	-0.0953	2.9043	-0.1837	0.058	0.0507	-0.0166	0.2931	0.3235	-0.3002	0.1565	-0.1094	0.2292	0.0979	-0.1222	0.1266	-0.0283	0.3968	68.722	47.3298	62.5632
7	0.0245	0.1505	0.1779	2.3733	4.2964	9.21	-0.0865	0.0309	-0.064	0.2952	0.2851	-0.4976	1.2925	0.7209	-0.1986	0.4879	0.1059	0.2838	0.2133	0.0055	0.5269	75.5294	16.4829	52.3568
8	2.3211	1.0568	0.1728	3.5557	1.4168	2.5405	-0.1877	-0.27	-0.2476	0.0528	0.1046	-0.1951	0.5801	0.1133	0.0831	0.2977	0.1384	0.0204	0.1443	0.053	0.1658	67.8571	12.7864	63.5096
9	1.3593	-0.1112	1.239	1.518	-1.9217	3.3259	-0.0926	-0.1126	-0.1456	-0.113	0.0517	-0.1376	0.0547	-0.15	0.0408	0.236	0.0463	0.0409	0.1483	0.0386	0.2442	68.1529	17.9043	57.2077
10	9.172	-0.5325	-8.2965	2.4811	3.4779	11.3899	-0.7594	-0.2955	-0.5776	0.1612	0.0625	0.242	1.0325	0.0703	0.6968	0.4685	-0.0755	-0.028	0.2116	0.1277	0.1553	60.0102	8.3811	54.1948
11	0.2486	-0.1785	0.1658	0.1659	0.0912	3.5212	-0.115	-0.065	-0.0874	0.0541	0.0696	0.1223	0.159	-0.2735	0.0454	0.2918	0.0054	0.019	0.203	0.0477	0.2285	59.8945	20.5493	54.5977
12	3.0522	0.7526	0.6312	2.214	0.6427	1.9037	0.0032	-0.0881	0.0084	-0.0504	0.0255	0.3646	0.2035	-0.2093	-0.0287	0.1823	0.0762	0.0219	0.2172	0.0397	0.2263	51.4147	23.5124	66.7352
13	18.1202	-2.2837	1.3535	0.4379	-0.2222	0.1198	0.3764	0.0533	-0.1408	0.052	-0.2315	0.2985	-0.0088	0.0561	-0.1448	0.1227	-0.1116	0.1776	0.4711	-0.2803	0.5605	31.8304	16.1323	18.0755
14	2.2311	0.6333	0.2388	2.3462	0.2254	1.8052	0.0969	0.0609	-0.2282	0.1876	-0.2495	0.1319	0.2542	-0.1908	0.1526	0.1085	-0.1131	0.0454	0.3086	-0.1046	0.184	38.1794	6.1632	20.2626
15	0.8777	0.4489	0.3378	1.8386	1.093	2.5014	-0.1049	0.1052	-0.1537	0.0399	0.07	-0.1619	0.3523	-0.0453	0.0349	0.2358	-0.055	0.0395	0.1875	-0.0205	0.2144	60.1527	6.446	23.332
16	9.5867	9.9404	-15.3119	27.0462	-4.1882	32.6381	0.1094	-0.8482	-0.4308	0.4649	-0.4286	-1.0514	0.3391	1.5785	0.3192	0.2223	-0.0993	-0.0431	0.3383	0.0123	0.2236	54.8448	-4.6643	12.8645
17	1.192	-0.7132	0.0416	1.3393	0.8973	2.7984	0.0253	0.1953	-0.1609	0.0646	-0.0417	0.0235	0.2833	-0.2931	0.0165	0.1872	-0.1416	0.034	0.2025	-0.0348	0.1993	53.8471	2.4649	17.1211
18	3.3903	-0.1083	-1.4142	1.14	0.9005	5.6158	-0.1136	0.0728	-0.2449	0.2976	0.0807	-0.3153	0.4928	0.453	0.0329	0.25	-0.0206	-0.0007	0.0774	-0.018	0.2063	67.1326	2.5732	25.4106
19	13.2147	2.4295	4.5317	6.2741	-5.5179	8.5079	-0.3719	0.7506	-0.4027	-0.2042	0.6846	0.1589	-0.0608	-0.3816	-0.3128	0.3123	-0.0795	-0.1311	0.4536	-0.1191	0.1389	56.0018	23.523	4.7262
20	2.6485	0.283	-0.1752	1.3583	0.4981	3.2037	-0.1864	0.5827	0.1536	-0.3701	0.1425	0.4025	-0.481	-0.3576	0.0439	0.1737	-0.0336	-0.0602	0.2917	0.0419	0.1897	51.8355	29.9589	15.7381
21	2.9011	1.6123	0.7858	3.1371	2.3481	1.8468	-0.312	0.37	0.0823	-0.3129	0.0992	0.2373	-0.2043	-0.039	0.2128	0.1845	-0.0175	-0.0522	0.3027	0.059	0.2072	58.3628	25.8904	13.3065
22	0.4338	0.1055	0.6038	2.5482	0.6744	3.4651	-0.1935	0.232	0.1913	-0.1977	0.1279	0.1414	-0.5252	-0.2392	0.0657	0.2045	-0.0339	-0.0635	0.2899	0.1061	0.2054	60.7313	37.8455	15.3925
23	3.2297	-1.5191	-1.5568	0.9819	0.9917	5.5097	-0.1797	0.1263	0.1387	0.019	0.2266	-0.1342	-0.0142	0.2239	-0.0469	0.1668	-0.1181	0.0042	0.3155	-0.0113	0.2297	66.9306	26.49	16.3859
24	1.8524	0.4218	-0.0003	1.7878	-0.3757	2.2516	0.0186	-0.0211	0.1632	0.2103	-0.0006	0.0753	-0.3062	0.0552	-0.018	0.2089	-0.0049	-0.0057	0.1367	0.014	0.1803	63.2459	29.8208	31.8025

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	196 - 206
2	X-RAY DIFFRACTION	2	A	207 - 275
3	X-RAY DIFFRACTION	3	A	276 - 313
4	X-RAY DIFFRACTION	4	A	314 - 383
5	X-RAY DIFFRACTION	5	A	384 - 425
6	X-RAY DIFFRACTION	6	A	426 - 445
7	X-RAY DIFFRACTION	7	B	1 - 15
8	X-RAY DIFFRACTION	8	B	16 - 43
9	X-RAY DIFFRACTION	9	B	44 - 62
10	X-RAY DIFFRACTION	10	B	63 - 83
11	X-RAY DIFFRACTION	11	B	84 - 114
12	X-RAY DIFFRACTION	12	B	115 - 161
13	X-RAY DIFFRACTION	13	C	196 - 206
14	X-RAY DIFFRACTION	14	C	207 - 263
15	X-RAY DIFFRACTION	15	C	264 - 306
16	X-RAY DIFFRACTION	16	C	307 - 312
17	X-RAY DIFFRACTION	17	C	313 - 388
18	X-RAY DIFFRACTION	18	C	389 - 445
19	X-RAY DIFFRACTION	19	D	2 - 15
20	X-RAY DIFFRACTION	20	D	16 - 43
21	X-RAY DIFFRACTION	21	D	44 - 62
22	X-RAY DIFFRACTION	22	D	63 - 87
23	X-RAY DIFFRACTION	23	D	88 - 112
24	X-RAY DIFFRACTION	24	D	113 - 161

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