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

ID or keywords:

Entry

Database: PDB / ID: 4kva

Title

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

Components

Septin

Keywords

HYDROLASE /

Small GTPase /

cytoskeleton component

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: 2.14 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	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4kva.cif.gz	228.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4kva.ent.gz	181.7 KB	Display	PDB format
PDBx/mmJSON format	4kva.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/4kva ftp://data.pdbj.org/pub/pdb/validation_reports/kv/4kva	HTTPS FTP

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Related structure data

Related structure data	4kv9C C: citing same article (ref.)
Similar structure data	4hg5-1 4g82-d 3ftq-6 3tw4-d 3exj-d 6mq9-6 6mqk-6 6mq9-5 4hg5-2 2odq-d 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

97.4 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)	160.800, 47.040, 95.480
Angle α, β, γ (deg.)	90.000, 112.610, 90.000
Int Tables number	5
Space group name H-M	C121

#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-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.73 Å³/Da / Density % sol: 28.93 %
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: I04-1 / Wavelength: 0.92
Detector	Type: PSI PILATUS 2M / Detector: PIXEL / Date: May 24, 2012
Radiation	Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 2.14→74.221 Å / Num. obs: 36348 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / R_sym value: 0.088 / Net I/σ(I): 9.9
Reflection shell	Resolution: 2.14→2.2 Å / Redundancy: 5 % / R_merge(I) obs: 0.785 / Mean I/σ(I) obs: 0.9 / R_sym value: 0.785 / % possible all: 99.5

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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: SCHISTOSOMA MANSONI SEPTIN 10 GTPASE DOMAIN

Resolution: 2.14→74.22 Å / Occupancy max: 1 / Occupancy min: 0.48 / SU ML: 0.26 / σ(F): 1.35 / Phase error: 24.99 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.221	1812	4.99 %
R_work	0.187	-	-
obs	0.187	36333	98.8 %

Solvent computation

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

Displacement parameters

B_iso mean: 43.63 Å²

Refinement step

Cycle: LAST / Resolution: 2.14→74.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4011	0	66	190	4267

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	4153
X-RAY DIFFRACTION	f_angle_d	0.592	5618
X-RAY DIFFRACTION	f_dihedral_angle_d	16.775	1550
X-RAY DIFFRACTION	f_chiral_restr	0.038	643
X-RAY DIFFRACTION	f_plane_restr	0.002	704

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 (%)
2.141-2.1989	0.2866	133	0.2566	2626	X-RAY DIFFRACTION	99
2.1989-2.2636	0.2893	129	0.2359	2675	X-RAY DIFFRACTION	99
2.2636-2.3367	0.2871	145	0.2346	2614	X-RAY DIFFRACTION	99
2.3367-2.4202	0.2569	136	0.2159	2655	X-RAY DIFFRACTION	100
2.4202-2.5171	0.2517	122	0.2167	2666	X-RAY DIFFRACTION	99
2.5171-2.6317	0.2832	141	0.2172	2667	X-RAY DIFFRACTION	99
2.6317-2.7705	0.2713	138	0.2062	2610	X-RAY DIFFRACTION	98
2.7705-2.944	0.2605	164	0.2096	2564	X-RAY DIFFRACTION	96
2.944-3.1714	0.2508	135	0.2113	2677	X-RAY DIFFRACTION	100
3.1714-3.4905	0.2136	128	0.1892	2677	X-RAY DIFFRACTION	99
3.4905-3.9956	0.207	134	0.1701	2679	X-RAY DIFFRACTION	99
3.9956-5.0338	0.1746	170	0.1425	2665	X-RAY DIFFRACTION	99
5.0338-74.2653	0.1827	137	0.1675	2746	X-RAY DIFFRACTION	98

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	5.188	1.2744	-0.1805	5.1819	-0.564	8.6593	-0.1875	-0.1837	-0.347	-0.1207	-0.1176	-0.1479	0.3328	0.1506	0.2551	0.2239	0.0067	0.0316	0.2078	-0.0019	0.2169	-48.7814	-19.6585	111.3811
2	5.7906	-1.7013	-0.1988	7.7964	-5.2297	7.2422	-0.1883	0.404	-1.1227	-0.8718	0.0301	-0.4551	1.42	0.975	0.5447	0.6248	0.072	0.0394	0.3947	-0.1195	0.5688	-49.0098	-27.0654	106.9706
3	3.8452	-0.3274	3.3763	0.3116	0.8864	5.1615	-0.0451	0.4456	-0.2059	-0.0508	0.1352	-0.1891	-0.0934	0.3603	0.0188	0.2596	-0.0294	0.0287	0.2258	0.0431	0.2664	-55.168	-14.4269	102.2547
4	1.9259	0.813	0.0046	1.9912	1.9673	2.7912	0.0305	-0.3682	0.3362	-0.0633	0.0314	0.0328	-0.1425	0.0458	0.1044	0.2351	-0.0498	0.0264	0.1498	0.0587	0.187	-47.665	-8.7223	114.0986
5	7.1777	-6.8891	5.9935	8.0754	-5.9992	5.3741	-0.4121	-0.1932	1.3175	0.0697	-0.2602	0.0717	-0.877	0.6888	0.3788	0.401	-0.0929	-0.014	0.4256	-0.0435	0.4524	-44.5208	0.4785	120.2102
6	6.5463	0.2662	-0.0345	3.1607	-1.2554	6.5124	-0.0716	-0.7835	0.7474	0.153	-0.1301	0.5205	-0.6377	-0.8334	0.0753	0.26	0.0625	-0.0604	0.3393	-0.1079	0.2971	-62.134	-5.6933	118.5479
7	2.8226	0.3464	1.1111	3.2424	-0.4182	4.923	0.0085	-0.7785	0.0647	0.101	-0.1631	-0.1128	-0.1505	-0.1205	0.2451	0.2674	-0.029	-0.0023	0.3677	0.0313	0.1972	-51.9578	-11.6138	123.5062
8	5.7392	-1.9705	2.0599	2.1539	0.1389	2.4938	-0.0716	-0.7618	-1.077	0.4469	-0.1887	0.2674	0.3966	0.2345	0.0697	0.3516	0.0312	0.0765	0.5803	0.236	0.4663	-39.9358	-20.567	127.7786
9	5.8016	-1.0379	5.314	0.2307	-1.0501	8.9981	-0.0856	-0.4346	-0.2306	0.1109	0.1337	0.0647	-0.1571	-0.4768	-0.062	0.2471	-0.0201	0.0287	0.1387	-0.0042	0.2693	-63.7033	-12.8744	107.8794
10	8.4909	2.9191	1.6467	5.0968	1.2331	6.5131	0.1029	-0.6213	0.6771	0.1652	-0.106	0.2649	-0.4804	-0.3813	-0.001	0.2722	0.0262	0.0377	0.3382	-0.0145	0.2681	-18.0213	3.5261	116.1121
11	2.5434	0.4116	-2.4926	3.6238	-2.1827	4.6733	-0.1527	0.0839	0.3139	-0.052	0.2822	0.4375	0.0307	-0.4619	-0.0863	0.2454	0.0462	0.015	0.2619	-0.0123	0.2519	-14.7204	4.706	103.8634
12	4.0804	5.0334	-3.8898	6.836	-4.0437	4.5703	0.7421	-1.253	0.6216	0.8447	-0.8984	0.1916	-0.8863	0.7207	-0.0642	0.3474	-0.0523	-0.0244	0.3576	-0.0449	0.3563	-1.4868	10.865	104.5486
13	2.8906	3.2384	-3.7298	6.0318	-3.1434	6.1323	-0.2279	0.3019	-0.4213	-0.3064	0.2062	0.4101	0.75	-0.8002	0.0873	0.2577	-0.0492	-0.0187	0.3978	-0.0093	0.2945	-23.2616	-10.2983	104.4236
14	3.514	1.3371	-1.4524	3.2108	-1.2503	2.9252	-0.353	-0.2272	-0.5977	-0.1489	0.1395	-0.1234	0.3373	0.0317	0.1966	0.2313	0.0015	-0.0053	0.314	0.0717	0.2649	-20.1933	-10.5854	110.5835
15	4.7182	1.1898	-4.2237	2.9449	-1.1348	8.5574	-0.8115	0.0982	-1.4054	-0.4465	0.239	0.0716	1.254	-0.8617	0.3133	0.4247	-0.036	0.0799	0.3585	0.0476	0.5429	-23.3885	-21.7634	109.9108
16	5.5234	-0.3892	1.0618	3.6168	-1.3368	4.3318	0.0384	-0.2631	-1.0251	-0.1824	-0.2011	-1.1274	1.3639	0.5375	-0.0307	0.3375	0.0876	0.0944	0.4464	0.1068	0.5987	-6.7551	-14.9105	108.0765
17	0.7278	0.7765	-0.34	1.1626	-1.1639	1.9434	0.0659	-0.3148	-0.2661	0.239	-0.2926	-0.2277	-0.0379	-0.0035	0.1208	0.3148	-0.0254	-0.0418	0.6282	0.1433	0.3181	-18.1577	-10.622	124.8324
18	6.326	2.8045	-5.8881	1.1557	-2.5778	6.4064	0.1286	-1.4638	-0.2072	0.1134	-0.3682	-0.205	0.1584	0.988	0.3544	0.3126	0.0032	-0.0104	0.6279	0.1177	0.3584	-12.8917	-9.0517	120.0054
19	6.3483	3.1632	-6.4368	2.0877	-2.8567	9.0482	-0.0608	0.1426	0.3667	-0.3045	0.2061	0.0762	-0.4161	-0.4824	-0.3463	0.3033	-0.0147	-0.0366	0.1813	-0.001	0.2818	-4.2449	2.2142	92.074

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 87 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 88 through 172 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 173 through 189 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 190 through 206 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 207 through 221 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 222 through 241 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 242 through 269 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 270 through 306 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 40 through 89 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 90 through 133 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 134 through 148 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 149 through 172 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 173 through 189 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 190 through 206 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 207 through 221 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 222 through 255 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 256 through 291 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 292 through 306 )

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