PDB-4kv9: GTPase domain of Septin 10 from Schistosoma mansoni in complex wi...

ID or keywords:

Entry

Database: PDB / ID: 4kv9

Title

GTPase domain of Septin 10 from Schistosoma mansoni in complex with GDP

Components

Septin

Keywords

HYDROLASE /

Small GTPase /

cytoskeleton component / septins

Function / homology

Function and homology information

septin complex / protein homooligomerization / GDP binding / vesicle / protein heterodimerization activity / GTP binding / magnesium ion binding / protein homodimerization activity / identical protein binding
Similarity search - Function

Biological species

Schistosoma mansoni (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.93 Å

Authors

Zeraik, A.E. / Pereira, H.M. / Santos, Y.V. / Brandao-Neto, J. / Garratt, R.C. / Araujo, A.P.U. / Demarco, R.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Crystal Structure of a Schistosoma mansoni Septin Reveals the Phenomenon of Strand Slippage in Septins Dependent on the Nature of the Bound Nucleotide.
Authors: Zeraik, A.E. / Pereira, H.M. / Santos, Y.V. / Brandao-Neto, J. / Spoerner, M. / Santos, M.S. / Colnago, L.A. / Garratt, R.C. / Araujo, A.P. / Demarco, R.

History

Deposition	May 22, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2014	Group: Database references
Revision 1.2	Apr 2, 2014	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4kv9.cif.gz	223.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4kv9.ent.gz	178.4 KB	Display	PDB format
PDBx/mmJSON format	4kv9.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/kv/4kv9 ftp://data.pdbj.org/pub/pdb/validation_reports/kv/4kv9	HTTPS FTP

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Related structure data

Related structure data	4kvaC 2qnrS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6i49-d 6hzh-d 4h5u-2 5a8b-d 6fzu-d 6jc3-d 2oqf-d 5vro-d 6e3g-d 3lk4-5 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: Septin

B: Septin

hetero molecules

97.2 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)	160.900, 45.050, 95.490
Angle α, β, γ (deg.)	90.000, 112.170, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-641- HOH

#1: Protein	Septin / Mass: 48156.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Septin 10, Smp_029890 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G4VFI8
#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.66 Å³/Da / Density % sol: 26.07 %
Crystal grow	Temperature: 293 K / pH: 7.3 Details: 0.2 M sodium acetate, 25% PEG 3350, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2012
Radiation	Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9686 Å / Relative weight: 1
Reflection	Resolution: 1.93→26.17 Å / Num. obs: 47003 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / R_sym value: 0.048 / Net I/σ(I): 10
Reflection shell	Resolution: 1.93→1.98 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.633 / Mean I/σ(I) obs: 1.2 / R_sym value: 0.633 / % possible all: 96.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHASER		phasing
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.11	data extraction
GDA		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QNR

2qnr

Resolution: 1.93→26.17 Å / Occupancy max: 1 / Occupancy min: 0.35 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 28.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.217	2375	5.06 %
R_work	0.184	-	-
obs	0.185	46962	97.4 %

Solvent computation

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

Displacement parameters

B_iso mean: 53.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.93→26.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3928	0	56	129	4113

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4097
X-RAY DIFFRACTION	f_angle_d	1.185	5560
X-RAY DIFFRACTION	f_dihedral_angle_d	16.12	1518
X-RAY DIFFRACTION	f_chiral_restr	0.077	650
X-RAY DIFFRACTION	f_plane_restr	0.005	700

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 (%)
1.93-1.9694	0.3738	134	0.3803	2553	X-RAY DIFFRACTION	95
1.9694-2.0122	0.3659	128	0.3473	2557	X-RAY DIFFRACTION	96
2.0122-2.059	0.4139	154	0.3258	2562	X-RAY DIFFRACTION	96
2.059-2.1105	0.3798	127	0.3051	2580	X-RAY DIFFRACTION	96
2.1105-2.1675	0.2932	129	0.2734	2581	X-RAY DIFFRACTION	97
2.1675-2.2312	0.295	135	0.2419	2609	X-RAY DIFFRACTION	97
2.2312-2.3032	0.2674	143	0.2361	2560	X-RAY DIFFRACTION	97
2.3032-2.3855	0.2986	130	0.2184	2607	X-RAY DIFFRACTION	96
2.3855-2.4809	0.2178	139	0.2116	2564	X-RAY DIFFRACTION	97
2.4809-2.5937	0.2345	145	0.1954	2597	X-RAY DIFFRACTION	97
2.5937-2.7304	0.2605	148	0.1889	2613	X-RAY DIFFRACTION	97
2.7304-2.9012	0.2444	147	0.1925	2637	X-RAY DIFFRACTION	98
2.9012-3.1249	0.23	133	0.2017	2666	X-RAY DIFFRACTION	99
3.1249-3.4387	0.2445	152	0.1822	2687	X-RAY DIFFRACTION	99
3.4387-3.9349	0.2169	148	0.1675	2682	X-RAY DIFFRACTION	99
3.9349-4.952	0.1443	147	0.1346	2731	X-RAY DIFFRACTION	100
4.952-26.1715	0.1656	136	0.1562	2801	X-RAY DIFFRACTION	99

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	4.8118	-0.3717	0.5149	3.4341	0.2459	4.6064	-0.0669	0.1925	-0.4632	-0.0842	0.0036	-0.087	0.3417	-0.0896	0.08	0.3997	-0.0243	-0.0044	0.4436	0.0269	0.3608	-12.3202	-19.2047	23.3739
2	7.7925	0.1697	1.2364	3.3715	-1.7997	5.916	0.0199	0.7347	-1.5625	0.3139	0.1532	-0.2815	0.6156	-0.4201	-0.2535	0.832	-0.0312	0.0534	0.386	-0.1289	0.7448	-15.5971	-27.6099	22.0711
3	9.9859	3.54	-3.4336	7.5255	-2.5906	2.4363	0.5625	0.9734	-0.8543	0.1653	-0.3902	-0.2632	-0.1513	0.3532	-0.2323	0.5706	-0.0103	-0.0368	0.4791	0.0297	0.4601	-14.7228	-20.0706	17.7985
4	8.2487	0.7678	5.5994	0.2316	0.9618	6.216	-0.0772	0.4202	-0.3446	-0.0121	0.132	-0.174	-0.0086	0.3404	-0.0126	0.3635	-0.0117	-0.0073	0.2873	0.0262	0.3197	-21.2814	-14.3042	13.1493
5	6.9534	-0.7819	2.7587	0.7466	0.1805	3.2321	-0.1812	-0.0642	0.77	-0.1365	-0.0398	0.0055	-0.4198	0.0528	0.2117	0.3902	-0.0525	-0.0225	0.3361	0.0487	0.3695	-11.2457	-5.8541	22.51
6	2.367	-1.8393	1.6446	4.1052	-3.8381	3.2359	-0.5418	-1.3145	1.2075	-0.0132	0.1963	-0.3651	-0.878	0.1641	0.4778	0.4938	-0.0525	-0.0526	0.5221	-0.0607	0.4996	-7.8662	0.902	32.2094
7	4.1056	0.9981	0.892	0.9277	-1.4699	4.5479	0.0409	-0.6113	0.1389	0.024	-0.0584	0.0377	-0.0464	-0.5139	-0.0487	0.3903	-0.0377	-0.0107	0.4928	-0.0104	0.3287	-17.9896	-10.6308	34.2677
8	7.1241	0.3609	0.7607	0.0363	-1.3085	1.5756	0.1281	-0.7686	-0.6925	-0.0728	-0.2637	-0.0892	0.2999	0.0522	0.1517	0.4167	0.0015	0.0252	0.669	0.1704	0.4479	-7.8464	-18.4984	38.0312
9	3.7223	-0.7984	3.6001	1.6609	0.2292	4.0285	-0.032	-0.2249	0.1982	0.0947	0.0539	0.06	-0.4352	-0.3923	0.052	0.2423	-0.0375	-0.0031	0.2805	0.0122	0.2974	-30.0728	-10.5196	15.1939
10	2.1188	1.0686	-2.6708	5.3843	-2.751	4.0392	0.4276	-0.1388	0.1539	0.0419	-0.1176	0.1333	-0.1942	0.0316	-0.2591	0.3538	0.011	-0.0136	0.4548	-0.0499	0.2875	19.0559	-0.176	23.6489
11	5.4599	2.2536	4.9753	7.3694	-0.0333	5.1665	-0.2002	-0.814	0.6421	0.5657	-0.3509	0.2438	-1.0623	-0.0507	0.4389	0.3735	-0.0087	-0.0122	0.5331	0.005	0.3242	16.7594	-0.8412	31.5944
12	4.0614	-1.1915	1.463	7.6603	-7.0307	6.4662	0.0679	-1.7664	0.9622	0.2628	-0.3212	-0.0901	-1.1898	0.4184	-0.0815	0.8429	-0.0559	-0.0028	0.8156	-0.1889	0.6444	16.8556	7.71	31.7713
13	2.5405	0.7349	-1.6586	7.747	0.0919	6.637	0.3093	-1.3434	1.2223	0.8365	-0.3714	-0.3639	-0.8702	0.2363	-0.0979	0.8307	-0.0667	-0.0618	0.6743	-0.077	0.6138	24.27	7.5931	29.5873
14	6.7977	5.115	5.6075	3.8202	4.1181	4.9155	0.5018	-0.2093	1.0231	0.1454	-0.4131	0.1883	-0.0587	-0.4255	0.057	0.5364	0.0514	-0.015	0.5404	0.0142	0.4534	18.7048	4.0235	22.8379
15	3.3942	3.3265	-4.2275	6.747	-2.391	5.7558	-0.0359	0.7333	0.9277	0.0639	0.3613	0.529	-0.3632	-0.4339	-0.3498	0.3505	0.0552	0.0043	0.2847	-0.0002	0.3431	23.5319	5.6488	10.3517
16	7.6398	4.7591	-4.523	4.4924	-4.0732	2.9977	0.5023	-0.9111	0.7473	0.4893	-0.4414	0.2945	-0.619	0.3768	-0.0693	0.4294	-0.0359	0.0018	0.4069	-0.0756	0.4115	29.6284	5.6941	17.8011
17	5.6595	0.1462	-2.6655	3.6132	1.2915	7.9972	-0.5931	0.1643	-0.6497	-0.4123	0.1158	0.5959	1.1954	-0.8235	0.4753	0.4136	-0.08	-0.0173	0.4639	-0.0096	0.4113	11.857	-11.5593	14.1928
18	3.6567	0.7746	-1.0627	2.5794	-1.248	1.328	-0.2691	-0.3542	-0.4394	-0.233	0.1055	-0.0657	0.4193	-0.115	0.1357	0.3532	-0.0079	-0.0172	0.3724	0.0691	0.3413	16.3915	-10.4472	22.1521
19	7.6864	-0.674	-2.8213	1.2793	-0.9611	9.9354	-0.8383	-0.0381	-1.1631	-0.8165	0.4774	0.0647	1.4701	-0.6259	0.3723	0.6336	-0.0616	0.1483	0.3034	0.0441	0.6292	13.2929	-21.2035	20.5843
20	8.5279	-0.1196	2.6223	6.3283	-1.5948	8.4718	-0.1753	0.2073	-1.3549	0.0168	-0.0268	-1.0425	0.9006	1.5714	-0.0777	0.5905	0.1595	0.1648	0.5734	0.1763	0.844	29.6586	-14.9924	19.5892
21	2.502	0.0235	-0.9534	2.4702	-1.2811	2.7177	-0.3932	-0.7811	-0.5685	0.2539	-0.1923	-0.6136	0.9238	0.7481	0.4092	0.4695	0.1174	0.0437	0.6783	0.2598	0.5755	22.6297	-14.4155	29.5424
22	1.5014	-1.5885	2.4924	4.5246	0.5809	8.2802	-0.2758	-0.788	-0.0731	0.4783	-0.0494	-0.5112	-1.0681	0.169	0.2239	0.6629	-0.1391	-0.0525	0.9752	0.1374	0.4059	12.7219	-6.2481	44.604
23	5.211	1.984	-3.8569	0.5107	-1.6321	5.0862	0.2472	-1.6477	-0.0495	0.1762	-0.3512	-0.1096	-0.085	1.0063	0.1168	0.3996	0.0481	-0.0006	0.786	0.1512	0.4556	23.8546	-9.3522	31.5967
24	5.1735	-2.0676	0.0504	3.9509	-0.9604	7.6249	-0.1226	0.3671	0.109	-0.3745	0.0231	0.1465	-0.333	-0.0625	0.0983	0.3713	-0.0354	-0.0262	0.2943	-0.0226	0.3441	32.1404	2.5419	3.9444

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 40 through 62 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 91 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 102 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 111 through 162 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 163 through 189 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 190 through 206 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 207 through 245 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 249 through 278 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 279 through 306 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 40 through 53 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 54 through 62 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 63 through 70 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 79 through 91 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 92 through 102 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 109 through 133 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 134 through 154 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 155 through 172 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 173 through 189 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 190 through 206 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 207 through 221 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 222 through 241 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 242 through 255 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 256 through 291 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 292 through 306 )

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