PDB-2w1j: CRYSTAL STRUCTURE OF SORTASE C-1 (SRTC-1) from Streptococcus pneu...

ID or keywords:

Entry

Database: PDB / ID: 2w1j

Title

CRYSTAL STRUCTURE OF SORTASE C-1 (SRTC-1) from Streptococcus pneumoniae

Components

PUTATIVE SORTASE

Keywords

TRANSFERASE / PATHOGENICITY

Function / homology

Function and homology information

membrane => GO:0016020 / hydrolase activity / membrane
Similarity search - Function

Biological species

STREPTOCOCCUS PNEUMONIAE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.24 Å

Authors

Manzano, C. / Contreras-Martel, C. / El Mortaji, L. / Izore, T. / Fenel, D. / Vernet, T. / Schoehn, G. / Di Guilmi, A.M. / Dessen, A.

Citation

Journal: Structure / Year: 2008
Title: Sortase-Mediated Pilus Fiber Biogenesis in Streptococcus Pneumoniae.
Authors: Manzano, C. / Contreras-Martel, C. / El Mortaji, L. / Izore, T. / Fenel, D. / Vernet, T. / Schoehn, G. / Di Guilmi, A.M. / Dessen, A.

History

Deposition	Oct 17, 2008	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 23, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Mar 6, 2013	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Refinement description
Revision 1.3	May 15, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2w1j.cif.gz	102.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2w1j.ent.gz	80.1 KB	Display	PDB format
PDBx/mmJSON format	2w1j.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/w1/2w1j ftp://data.pdbj.org/pub/pdb/validation_reports/w1/2w1j	HTTPS FTP

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Related structure data

Related structure data	2w1kC C: citing same article (ref.)
Similar structure data	1wy7-1 3rbk-1 6t22-2 6lip-d 5zjc-d 2wts-1 6d1g-d 5syn-1 1rd4-3 3g66-2 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: PUTATIVE SORTASE

B: PUTATIVE SORTASE

hetero molecules

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

1

A: PUTATIVE SORTASE

hetero molecules

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

2

B: PUTATIVE SORTASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	68.091, 70.189, 86.542
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	PUTATIVE SORTASE / SORTASE C-1 Mass: 23755.898 Da / Num. of mol.: 2 / Fragment: RESIDUES 17-228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PLIM (PROTEIN EXPERT, GRENOBLE) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): RIL CELLS (INVITROGEN) References: UniProt: Q97SB9, UniProt: A0A0H2UNQ9*PLUS, EC: 2.3.2.12
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 451 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	SIGNAL PEPTIDE AND TRANSMEMBRANE DOMAIN DELETED

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.1 Å³/Da / Density % sol: 41.44 % / Description: 4 WAVELENGTHS MAD EXPERIMENT
Crystal grow	Temperature: 293 K / pH: 8.5 Details: 100 MM TRIS-HCL PH 8.5, 200 MM MGCL2 HEXAHYDRATE, 30% W/V POLYETHYLENE GLYCOL 4000 AT 20C.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.931
Detector	Type: ADSC CCD / Detector: CCD / Date: May 4, 2007
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 1.24→48.85 Å / Num. obs: 114617 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 13 % / B_iso Wilson estimate: 17.31 Å² / R_sym value: 0.05 / Net I/σ(I): 33.5
Reflection shell	Resolution: 1.24→1.32 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 5.1 / R_sym value: 0.51 / % possible all: 93.9

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Processing

Software

Name	Version	Classification
REFMAC	5.4.0067	refinement
XDS		data reduction
XSCALE		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 1.24→48.85 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.962 / SU B: 1.202 / SU ML: 0.026 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.185	5868	5.1 %	RANDOM
R_work	0.171	-	-	-
obs	0.172	110290	100 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 11.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.14 Å²	0 Å²	0 Å²
2-	-	-0.04 Å²	0 Å²
3-	-	-	0.19 Å²

Refinement step

Cycle: LAST / Resolution: 1.24→48.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3065	0	36	451	3552

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	3229
X-RAY DIFFRACTION	r_bond_other_d	0.006	0.022	3229
X-RAY DIFFRACTION	r_angle_refined_deg	1.16	1.969	4390
X-RAY DIFFRACTION	r_angle_other_deg	1.16	1.969	4390
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.167	5	412
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.252	25.068	146
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.638	15	570
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.27	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	504
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	2408
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	0.671	1.5	1979
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.187	2	3230
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.893	3	1250
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.007	4.5	1149
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
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: 1.24→1.28 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.268	386
R_work	0.257	7837

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	5.2758	-1.7483	-0.6147	8.6847	1.1943	3.2966	0.0434	0.2104	0.4635	-0.6247	-0.1465	0.1253	-0.6123	-0.1704	0.103	0.1601	0.0286	-0.0728	0.04	0.0193	0.0155	-5.7865	13.6507	0.3598
2	4.6059	0.6308	4.0525	1.5597	0.9729	5.1808	-0.0522	0.1352	-0.0459	-0.1621	0.1402	-0.0539	0.0146	0.1253	-0.088	0.0794	-0.0036	0.028	0.0528	-0.0278	0.0793	6.2655	0.157	4.5715
3	1.0142	-0.1515	0.6559	6.5488	0.6809	0.5171	-0.1316	0.1376	0.088	-0.1106	0.2489	-0.3754	-0.233	0.2407	-0.1173	0.0431	-0.0176	0.0327	0.0399	-0.0582	0.0589	15.9516	17.0376	17.8586
4	5.412	2.7944	3.2416	4.7225	2.5141	14.347	-0.0706	0.0954	0.2326	-0.0191	0.138	-0.3611	0.0108	0.4512	-0.0673	0.0965	-0.0647	0.0518	0.1263	0.0054	0.1337	18.9326	23.5427	11.3385
5	4.9018	0.9994	1.7428	8.1181	-0.4884	2.6794	-0.1408	0.6712	0.4119	-0.6695	-0.0478	-0.3348	-0.4632	0.4647	0.1885	0.1024	-0.042	0.0461	0.1016	-0.0294	0.0588	13.2355	13.2768	3.3369
6	5.2255	-4.4588	2.3027	9.2017	-3.0538	4.6197	-0.0214	0.4296	0.4888	-0.438	0.0526	-0.1802	-0.298	-0.0264	-0.0312	0.1134	-0.0385	0.0209	0.0661	-0.0101	0.0546	4.6449	11.9705	0.7396
7	2.5818	-0.3511	-1.1799	1.1141	0.305	1.775	-0.0685	0.1549	0.0099	-0.1416	0.0461	0.0695	-0.1362	-0.0765	0.0224	0.1042	-0.0034	0.0055	0.0338	0.0066	0.0601	-1.1699	17.4144	12.4461
8	10.2266	-0.0122	-2.9408	3.2081	-1.1172	6.5235	0.0625	0.7499	0.3621	-0.3626	0.0873	-0.1166	-0.3995	-0.038	-0.1498	0.1607	-0.0425	0.0039	0.0571	0.0325	0.0997	8.7654	25.2057	8.0658
9	1.0981	0.1752	0.5013	2.3446	0.4609	1.678	-0.0318	0.0883	-0.0579	-0.0313	0.0949	-0.1248	-0.0374	0.1204	-0.063	0.0669	0.0059	0.0193	0.0494	-0.0199	0.0641	7.4445	9.3503	15.3837
10	1.3039	1.8799	-1.3204	2.983	-1.337	2.5153	-0.0331	0.0937	0.2365	-0.1586	0.1445	0.1969	-0.1978	-0.1192	-0.1114	0.0988	0.009	-0.0178	0.0042	0.0072	0.0819	0.1619	26.409	19.1584
11	0.8306	0.1295	0.1844	1.3378	1.4531	4.7292	-0.0135	0.0354	-0.0291	-0.0197	-0.0245	0.0662	0.0173	-0.1317	0.038	0.0626	0.0022	0.0069	0.0321	0.003	0.0669	-4.7828	8.9657	17.8104
12	9.2201	5.6	-1.1	4.5366	-0.4098	1.2887	0.0224	-0.1126	-0.2146	-0.0307	-0.057	-0.2984	0.0056	0.1474	0.0346	0.0736	0.0027	0.0008	0.0401	0.0026	0.0504	8.2308	16.2604	29.5806
13	3.017	2.4087	1.2421	6.4378	1.7451	1.7798	0.1079	-0.146	-0.1771	0.0553	-0.017	-0.3921	-0.007	0.1693	-0.0909	0.0639	0.0358	-0.0097	0.0474	-0.0193	0.078	12.3962	8.0155	25.0756
14	0.5092	0.5739	0.0146	3.4855	0.5843	0.5411	0.0257	0.0057	-0.0052	0.0557	0.0159	-0.1343	-0.0397	0.0408	-0.0415	0.0629	0.0035	0.0046	0.0294	0.0016	0.0506	5.8426	19.2097	24.6841
15	6.4711	1.267	-0.9199	4.0595	2.2558	2.2741	-0.0468	0.4934	0.1986	-0.3466	-0.1108	0.5449	-0.0932	-0.4922	0.1575	0.0593	0.0018	-0.0044	0.0353	-0.0119	0.0629	-8.5971	2.6475	17.5821
16	10.091	2.9964	-3.7818	5.0522	1.2952	2.8221	0.0154	-0.4787	-0.1871	-0.2879	0.3862	0.8168	0.1686	-0.7827	-0.4017	0.1369	0.0232	0.0059	0.2255	-0.0502	0.1285	-6.7188	25.451	61.1216
17	6.4993	-0.8263	1.8878	4.8861	2.3125	6.9018	-0.0346	-0.6116	0.2884	0.2884	-0.1086	0.021	0.0001	-0.4029	0.1432	0.0948	0.0187	-0.0252	0.1331	-0.0909	-0.026	3.3014	26.9368	65.1253
18	1.7914	0.8841	1.3063	6.1729	4.6319	6.2387	-0.0276	-0.2436	0.0522	0.073	0.0296	-0.0318	-0.0901	0.1157	-0.002	0.0122	0.0102	-0.024	0.1144	0.0122	0.0341	15.0121	15.3989	61.8186
19	4.0826	0.3841	0.3883	0.0855	0.153	0.312	0.0525	-0.1696	-0.2282	-0.0123	0.0003	-0.0223	0.1004	-0.1073	-0.0528	0.0475	0.0048	-0.0235	0.0524	0.047	0.0846	0.6552	2.2734	48.5721
20	6.7947	1.0487	2.6931	6.2187	1.9841	8.8745	0.0961	0.0603	-0.3586	0.1276	-0.0086	0.0464	0.5198	0.0092	-0.0876	0.0914	-0.0156	0.0072	0.0882	0.0519	0.0784	-5.5322	-1.2686	54.8878
21	5.9481	6.0727	3.7208	8.9628	2.6784	2.7818	0.465	-0.8209	0.0511	0.8454	-0.4378	0.4611	0.4046	-0.448	-0.0272	0.0655	-0.0192	-0.006	0.1501	0.0556	0.0125	3.2134	7.5186	63.6369
22	7.849	-1.8253	-1.8347	4.3028	0.9641	4.519	0.0662	-0.3639	0.0602	0.2175	0.0193	0.5266	-0.1473	-0.3637	-0.0855	0.0873	0.0032	-0.0027	0.1401	0.0102	0.0623	2.1396	16.5749	64.345
23	1.0455	-0.5463	0.6518	2.028	-1.3103	1.4883	-0.0523	-0.1973	0.0457	0.153	0.0107	0.0299	-0.1069	-0.0951	0.0416	0.0384	0.0113	0.0036	0.0943	-0.0022	0.035	-2.5228	19.5467	52.3762
24	3.5053	-1.242	-0.8924	8.2519	-2.4535	3.4021	0.0178	-0.3634	-0.0788	0.5871	-0.0137	0.2456	0.0676	-0.1303	-0.0041	0.0584	-0.0075	0.0184	0.1326	0.0199	0.0792	-9.2092	8.4101	57.4132
25	1.4604	-0.2041	0.1975	0.3196	0.0599	0.2219	-0.0053	-0.1327	-0.0869	0.0431	0.0109	0.0259	0.0265	-0.0436	-0.0056	0.035	0.0034	0.0038	0.0807	0.0169	0.0402	-0.4446	13.2089	49.6255
26	9.5517	2.045	-1.7268	3.3668	-0.3843	4.5396	-0.0166	0.1749	0.2238	-0.0785	0.0823	0.128	-0.2295	-0.1236	-0.0657	0.039	0.0123	-0.0041	0.0478	-0.0067	0.0383	-5.3148	20.4	37.6467
27	0.7636	0.1534	0.0981	1.0734	0.3444	1.3722	-0.0271	-0.0629	0.0262	0.0343	0.0383	-0.0611	-0.0413	0.0663	-0.0113	0.0432	0.0097	0.0004	0.0628	0.0026	0.0622	5.1047	20.9881	44.9618
28	14.8126	1.9153	4.9331	4.1542	-0.5026	1.9759	-0.0118	0.0275	-0.5422	-0.0906	0.1105	-0.0859	0.2736	-0.0742	-0.0988	0.0813	0	0.0108	0.0395	0.0077	0.0873	2.0062	0.8563	40.23
29	2.5901	0.5281	0.539	0.6197	0.1716	0.5616	0.0051	-0.0046	-0.1219	-0.0183	0.0064	0.0096	0.0227	-0.0388	-0.0115	0.0379	0.0026	0.0057	0.0421	0.0098	0.0382	0.4225	10.2291	41.0473
30	3.1181	0.1246	-0.0968	1.01	-0.7442	1.5992	-0.0412	-0.1643	0.2158	0.0939	0.1034	-0.0887	-0.2381	0.1001	-0.0621	0.0378	0.0043	-0.0041	0.0522	0.0003	0.0562	10.4223	24.2224	44.4893

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	20 - 32
2	X-RAY DIFFRACTION	2	A	33 - 52
3	X-RAY DIFFRACTION	3	A	53 - 61
4	X-RAY DIFFRACTION	4	A	62 - 68
5	X-RAY DIFFRACTION	5	A	69 - 73
6	X-RAY DIFFRACTION	6	A	74 - 81
7	X-RAY DIFFRACTION	7	A	82 - 101
8	X-RAY DIFFRACTION	8	A	102 - 107
9	X-RAY DIFFRACTION	9	A	108 - 130
10	X-RAY DIFFRACTION	10	A	131 - 146
11	X-RAY DIFFRACTION	11	A	147 - 165
12	X-RAY DIFFRACTION	12	A	166 - 173
13	X-RAY DIFFRACTION	13	A	174 - 185
14	X-RAY DIFFRACTION	14	A	186 - 208
15	X-RAY DIFFRACTION	15	A	209 - 214
16	X-RAY DIFFRACTION	16	B	19 - 24
17	X-RAY DIFFRACTION	17	B	25 - 32
18	X-RAY DIFFRACTION	18	B	33 - 52
19	X-RAY DIFFRACTION	19	B	53 - 61
20	X-RAY DIFFRACTION	20	B	62 - 68
21	X-RAY DIFFRACTION	21	B	69 - 74
22	X-RAY DIFFRACTION	22	B	75 - 81
23	X-RAY DIFFRACTION	23	B	82 - 101
24	X-RAY DIFFRACTION	24	B	102 - 107
25	X-RAY DIFFRACTION	25	B	108 - 142
26	X-RAY DIFFRACTION	26	B	143 - 147
27	X-RAY DIFFRACTION	27	B	148 - 171
28	X-RAY DIFFRACTION	28	B	172 - 177
29	X-RAY DIFFRACTION	29	B	178 - 205
30	X-RAY DIFFRACTION	30	B	206 - 213

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