PDB-4e94: Crystal structure of MccF-like protein from Streptococcus pneumoniae

ID or keywords:

Entry

Database: PDB / ID: 4.0E+94

Title

Crystal structure of MccF-like protein from Streptococcus pneumoniae

Components

MccC family protein

Keywords

HYDROLASE / MccF / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / Serine peptidase

Function / homology

Function and homology information

hydrolase activity / nucleotide binding
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.651 Å

Authors

Nocek, B. / Tikhonov, A. / Kwon, K. / Severinov, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of MccF-like protein from Streptococcus pneumoniae
Authors: Nocek, B. / Tikhonov, A. / Kwon, K. / Severinov, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Mar 20, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 9, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Oct 30, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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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Download

PDBx/mmCIF format	4e94.cif.gz	300.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4e94.ent.gz	243.7 KB	Display	PDB format
PDBx/mmJSON format	4e94.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/e9/4e94 ftp://data.pdbj.org/pub/pdb/validation_reports/e9/4e94	HTTPS FTP

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Related structure data

Related structure data	3gjz 3sr3 3tyx
Similar structure data	6wqp-1 6ui3-d 4v1s-1 4okm-3 4okz-3 4w84-2 7cju-1 5d9p-1 1qno-d 4v1r-1 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-IDP91761

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: MccC family protein

B: MccC family protein

hetero molecules

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

1

A: MccC family protein

hetero molecules

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

2

B: MccC family protein

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

Unit cell

Length a, b, c (Å)	108.323, 118.912, 51.737
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	MccC family protein Mass: 39431.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0182 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q97SY1, UniProt: A0A0H2UN46*PLUS
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.11 Å³/Da / Density % sol: 41.78 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 2.0 M Ammonium sulfate, pH 8.5, 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: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2012 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.65→40 Å / Num. obs: 80740 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / R_merge(I) obs: 0.067 / Net I/σ(I): 24
Reflection shell	Resolution: 1.65→1.68 Å / % possible all: 99.9

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
SHELX		model building
MLPHARE		phasing
ARP		model building
WARP		model building
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.651→28.668 Å / SU ML: 0.13 / σ(F): 1.33 / σ(I): 0 / Phase error: 16.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1753	3800	5.08 %	Random
R_work	0.1457	-	-	-
all	0.15	78620	-	-
obs	0.1472	74816	92.33 %	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.49 Å² / k_sol: 0.374 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.6298 Å²	-0 Å²	-0 Å²
2-	-	-0.648 Å²	0 Å²
3-	-	-	-1.9817 Å²

Refinement step

Cycle: LAST / Resolution: 1.651→28.668 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5433	0	23	769	6225

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5677
X-RAY DIFFRACTION	f_angle_d	1.119	7711
X-RAY DIFFRACTION	f_dihedral_angle_d	12.247	2112
X-RAY DIFFRACTION	f_chiral_restr	0.061	864
X-RAY DIFFRACTION	f_plane_restr	0.005	992

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6511-1.672	0.2452	73	0.1735	1452	X-RAY DIFFRACTION	51
1.672-1.694	0.2052	101	0.1715	1690	X-RAY DIFFRACTION	61
1.694-1.7172	0.2003	90	0.1668	1883	X-RAY DIFFRACTION	67
1.7172-1.7418	0.2101	129	0.1694	2045	X-RAY DIFFRACTION	73
1.7418-1.7678	0.2333	115	0.1673	2367	X-RAY DIFFRACTION	84
1.7678-1.7954	0.2122	114	0.1702	2461	X-RAY DIFFRACTION	88
1.7954-1.8248	0.2046	139	0.1671	2576	X-RAY DIFFRACTION	91
1.8248-1.8563	0.208	139	0.161	2637	X-RAY DIFFRACTION	93
1.8563-1.89	0.2007	138	0.1545	2673	X-RAY DIFFRACTION	96
1.89-1.9264	0.1972	165	0.1519	2751	X-RAY DIFFRACTION	97
1.9264-1.9657	0.1907	143	0.1482	2779	X-RAY DIFFRACTION	98
1.9657-2.0084	0.1691	151	0.1486	2800	X-RAY DIFFRACTION	99
2.0084-2.0551	0.2067	144	0.1391	2830	X-RAY DIFFRACTION	100
2.0551-2.1065	0.1741	162	0.1409	2812	X-RAY DIFFRACTION	100
2.1065-2.1634	0.1817	154	0.1363	2839	X-RAY DIFFRACTION	100
2.1634-2.2271	0.1639	154	0.1328	2811	X-RAY DIFFRACTION	100
2.2271-2.2989	0.1606	116	0.1307	2858	X-RAY DIFFRACTION	100
2.2989-2.3811	0.1648	156	0.1319	2839	X-RAY DIFFRACTION	100
2.3811-2.4763	0.1732	164	0.1394	2841	X-RAY DIFFRACTION	100
2.4763-2.589	0.1689	170	0.1458	2829	X-RAY DIFFRACTION	100
2.589-2.7254	0.1885	156	0.1522	2854	X-RAY DIFFRACTION	100
2.7254-2.896	0.1564	166	0.1445	2822	X-RAY DIFFRACTION	100
2.896-3.1193	0.1878	149	0.1462	2858	X-RAY DIFFRACTION	100
3.1193-3.4328	0.1757	136	0.1376	2923	X-RAY DIFFRACTION	100
3.4328-3.9284	0.1463	162	0.1332	2892	X-RAY DIFFRACTION	100
3.9284-4.9453	0.1496	150	0.1231	2918	X-RAY DIFFRACTION	99
4.9453-28.6723	0.1798	164	0.186	2976	X-RAY DIFFRACTION	97

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	1.8974	-0.538	-1.0531	1.2606	0.523	1.5953	-0.1228	0.0782	-0.0778	-0.0486	0.02	0.0385	0.2185	-0.0736	0.0335	0.1793	-0.0282	0.0026	0.1324	-0.0242	0.1243	28.8585	-10.6364	10.4326
2	8.8612	0.1408	-0.0385	0.9818	-0.9662	1.5991	0.0222	0.4706	0.1051	-0.3517	0.0241	0.166	0.2172	-0.4412	-0.0598	0.1803	0.0044	-0.0065	0.1958	-0.025	0.1203	30.616	-5.552	0.1472
3	3.143	0.5314	-0.8999	1.2466	0.8734	1.5365	-0.0737	0.0785	-0.2331	-0.0897	0.0258	-0.0559	0.2888	-0.1183	-0.0275	0.1814	0.0146	0.0009	0.1042	-0.0159	0.1308	35.9788	-14.1257	5.8658
4	2.5166	-0.0071	-0.1824	1.9335	-0.7396	3.9401	-0.0142	0.1184	-0.1153	-0.1548	-0.0222	0.4242	0.3545	-0.7491	0.0907	0.1613	-0.0814	-0.0094	0.2695	-0.0412	0.2077	16.615	-12.1469	11.7563
5	0.9762	-0.2846	-0.505	0.8377	-0.1852	1.882	-0.0041	-0.0318	-0.1767	0.0196	-0.086	0.1296	0.3552	-0.1859	0.079	0.2032	-0.0648	0.0139	0.1417	-0.0234	0.1573	25.7372	-13.7897	18.9967
6	4.8727	-5.3867	-1.9146	7.0953	0.4727	4.1607	-0.1721	-0.1977	-0.2715	0.1752	-0.1168	0.092	0.6235	-0.063	0.201	0.3959	-0.102	0.047	0.1744	0.0363	0.1841	25.4611	-21.2303	28.2116
7	0.7465	0.2064	-0.1531	0.9178	0.0044	2.3909	-0.0042	-0.0508	-0.0387	0.0649	-0.0286	0.0889	0.2647	-0.1156	0.029	0.141	-0.0163	0.0112	0.1051	-0.0198	0.111	31.7882	-6.8003	21.5994
8	0.2889	-0.0665	0.4338	0.6491	-0.0351	1.7008	-0.0041	0.0733	-0.0154	-0.0539	-0.037	-0.0146	0.0249	0.074	0.0389	0.0498	0.0062	0.0065	0.0967	-0.0047	0.0915	39.9707	5.1729	9.9717
9	0.9465	0.6506	-0.0215	1.3312	0.0863	1.2073	0.0671	-0.0362	0.04	0.0877	-0.085	0.0688	0.0707	-0.1767	-0.0233	0.0794	0.0063	0.0146	0.0946	-0.022	0.0652	28.8909	4.289	30.2159
10	2.191	1.3749	0.1301	0.8681	0.0814	0.0146	0.0723	-0.6547	0.2158	0.6697	-0.2621	0.2712	0.4501	-0.3414	-0.0552	0.2771	-0.1239	0.0779	0.3046	-0.0264	0.2117	18.1379	-8.7147	33.8509
11	0.8292	-0.319	0.4382	1.1337	-1.196	3.2786	-0.0646	-0.1331	0.0172	0.1385	0.1155	0.1682	-0.0728	-0.4015	-0.03	0.0652	0.0061	0.0069	0.1068	-0.0316	0.0899	28.8524	4.7805	30.4472
12	0.4794	0.116	-0.0344	0.4283	-0.6332	1.2098	-0.0366	-0.0306	0.0303	0.0608	0.0104	0.0521	-0.0354	-0.2123	0.0129	0.0933	0.0223	-0.0038	0.1255	-0.035	0.1049	29.5085	10.0693	30.4013
13	2.2753	-0.4283	1.2792	1.7611	-1.4055	2.5333	-0.0498	-0.1751	0.295	0.0402	-0.1233	-0.0321	-0.6585	-0.07	0.1667	0.1595	0.0291	-0.0102	0.1515	-0.0326	0.1378	31.55	18.5205	29.9706
14	0.641	0.3097	0.5506	1.432	-0.1366	1.5238	0.0099	-0.0813	0.035	0.0898	-0.0628	0.0374	0.0042	-0.0282	0.0722	0.0554	0.0042	0.0099	0.0941	-0.0049	0.1036	38.5697	6.0876	25.9618
15	1.303	0.851	-0.6907	5.7269	0.4323	1.9775	0.0484	-0.1151	-0.0324	0.3133	-0.0504	-0.4414	0.1592	0.3104	0.0009	0.1115	0.0372	-0.0259	0.139	-0.0067	0.1231	49.4037	2.5305	29.0363
16	0.9172	-0.3144	1.4431	1.4475	-0.415	3.085	0.0008	0.1133	-0.0388	-0.0496	0.0409	-0.1389	-0.083	0.2151	-0.0443	0.0889	0.0283	0.0111	0.1537	-0.0211	0.1376	17.8564	19.2514	-0.0235
17	2.2904	0.1613	1.6314	3.2837	-1.1979	3.9095	-0.0606	0.2797	0.1008	-0.1078	0.0447	-0.1989	-0.1797	0.4079	0.011	0.082	0.0445	-0.0004	0.1643	-0.0161	0.1433	25.6034	22.7419	5.6223
18	1.0115	0.1624	-0.0274	1.5154	0.2151	1.8597	0.1014	0.2498	-0.0394	-0.2392	-0.043	0.005	0.0893	0.2315	-0.0509	0.1985	0.0385	0.0108	0.2047	-0.042	0.167	16.1945	15.9672	-9.1578
19	1.6359	0.0188	1.7791	1.8383	-0.5146	3.4523	0.1555	0.0918	-0.1599	-0.0425	-0.0569	-0.0079	0.178	0.0204	-0.0759	0.1327	0.036	-0.0039	0.1319	-0.0223	0.1605	11.2829	15.8472	-0.9234
20	2.1839	0.7856	-0.8988	5.2357	-2.0673	3.2077	0.1563	0.0438	-0.4885	-0.0861	-0.1481	0.3646	0.5206	-0.0453	-0.0101	0.2295	-0.0003	-0.0518	0.1792	-0.0995	0.301	2.1101	8.544	-6.1794
21	2.0505	-0.124	0.6266	0.9195	0.2956	1.2133	0.0521	0.1361	-0.1363	0.0078	-0.0292	0.1164	0.0563	-0.0104	-0.0031	0.1118	0.0219	0.0042	0.0982	-0.0183	0.1539	6.1784	21.3509	3.0799
22	1.1328	-0.4897	-0.1672	1.8189	0.17	1.1156	-0.089	-0.1925	-0.0717	0.1991	0.1041	-0.0265	0.039	0.1409	-0.0082	0.1354	0.0288	0.0056	0.1057	0.0013	0.105	13.3594	29.2335	15.7478
23	4.2183	-2.1301	-2.0349	1.8498	0.2714	1.6827	0.2756	0.0313	0.2892	-0.2769	-0.1124	-0.348	-0.3095	0.2382	-0.1477	0.1977	-0.03	0.032	0.1577	-0.0098	0.2252	21.5766	40.4386	5.282
24	7.3906	3.6251	-1.1354	2.0273	-0.7295	0.5171	0.28	-0.0885	1.1881	0.0924	-0.1681	0.4505	-0.3533	-0.1169	-0.1841	0.1721	-0.0137	0.0423	0.1123	-0.0243	0.2037	3.8656	43.9931	14.5153
25	0.8854	-0.3831	-0.4524	0.9979	0.3931	2.0963	0.0115	0.1385	-0.101	-0.1604	-0.137	0.187	-0.077	-0.098	0.0781	0.1281	0.0091	-0.0203	0.1237	-0.0147	0.1635	-3.6038	31.2212	-1.4738
26	3.7993	-0.6046	-2.3092	8.3929	3.5284	2.6129	0.0413	0.4339	-0.5435	-0.2908	-0.0301	0.3592	0.0617	-0.5314	0.3307	0.1713	0.014	-0.0869	0.2663	-0.0964	0.263	-5.1868	19.0521	-10.8224
27	1.5589	0.38	-0.1806	1.4764	-0.0892	1.4871	0.0084	0.1309	0.0018	-0.1104	-0.0141	0.2405	-0.0669	-0.1154	0.0034	0.0922	0.0348	0.007	0.0834	-0.0069	0.1216	-3.4216	36.0492	-0.1422
28	5.5008	0.2235	-0.6216	1.5887	-0.7508	7.962	-0.1884	-0.1647	0.0687	0.1181	0.0779	0.3703	-0.4693	-1.0374	0.1478	0.2107	0.0835	0.0292	0.2183	-0.0045	0.2148	-10.2702	43.7957	2.8032
29	1.3292	-0.4699	-0.267	0.901	0.2917	0.5913	-0.0343	-0.0563	-0.0409	0.0849	-0.0196	0.107	-0.0153	-0.0357	0.0261	0.1305	0.0005	0.0263	0.0992	-0.0023	0.1133	0.1269	33.3197	12.2226
30	2.3563	1.1418	0.6329	3.0878	2.876	3.5989	-0.0843	-0.4562	-0.4465	0.4342	-0.1532	0.5588	0.303	-0.2673	0.0174	0.1162	-0.0199	0.1065	0.1355	0.0576	0.2546	-1.3803	27.8179	19.2078

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:17)
2	X-RAY DIFFRACTION	2	(chain A and resid 18:31)
3	X-RAY DIFFRACTION	3	(chain A and resid 32:42)
4	X-RAY DIFFRACTION	4	(chain A and resid 43:57)
5	X-RAY DIFFRACTION	5	(chain A and resid 58:91)
6	X-RAY DIFFRACTION	6	(chain A and resid 92:101)
7	X-RAY DIFFRACTION	7	(chain A and resid 102:135)
8	X-RAY DIFFRACTION	8	(chain A and resid 136:192)
9	X-RAY DIFFRACTION	9	(chain A and resid 193:226)
10	X-RAY DIFFRACTION	10	(chain A and resid 227:234)
11	X-RAY DIFFRACTION	11	(chain A and resid 235:259)
12	X-RAY DIFFRACTION	12	(chain A and resid 260:289)
13	X-RAY DIFFRACTION	13	(chain A and resid 290:301)
14	X-RAY DIFFRACTION	14	(chain A and resid 302:328)
15	X-RAY DIFFRACTION	15	(chain A and resid 329:343)
16	X-RAY DIFFRACTION	16	(chain B and resid 2:17)
17	X-RAY DIFFRACTION	17	(chain B and resid 18:39)
18	X-RAY DIFFRACTION	18	(chain B and resid 40:63)
19	X-RAY DIFFRACTION	19	(chain B and resid 64:86)
20	X-RAY DIFFRACTION	20	(chain B and resid 87:101)
21	X-RAY DIFFRACTION	21	(chain B and resid 102:135)
22	X-RAY DIFFRACTION	22	(chain B and resid 136:167)
23	X-RAY DIFFRACTION	23	(chain B and resid 168:187)
24	X-RAY DIFFRACTION	24	(chain B and resid 188:193)
25	X-RAY DIFFRACTION	25	(chain B and resid 194:226)
26	X-RAY DIFFRACTION	26	(chain B and resid 227:235)
27	X-RAY DIFFRACTION	27	(chain B and resid 236:293)
28	X-RAY DIFFRACTION	28	(chain B and resid 294:304)
29	X-RAY DIFFRACTION	29	(chain B and resid 305:334)
30	X-RAY DIFFRACTION	30	(chain B and resid 335:341)

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