PDB-5vcu: Crystal structure of ras-related c3 botulinum toxin substrate 1 i...

ID or keywords:

Entry

Database: PDB / ID: 5vcu

Title

Crystal structure of ras-related c3 botulinum toxin substrate 1 isoform x2 from Naegleria fowleri in complex with GDP

Components

Ras-related c3 botulinum toxin substrate 1 isoform x2

Keywords

SIGNALING PROTEIN / SSGCID / RAS /

botulinum toxin / GTP / GDP /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

small GTPase-mediated signal transduction /

GTPase activity / GTP binding
Similarity search - Function

Biological species

Naegleria fowleri (brain-eating amoeba)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of ras-related c3 botulinum toxin substrate 1 isoform x2 from Naegleria fowleri in complex with GDP
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Mar 31, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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 / pdbx_struct_conn_angle / struct_conn 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5vcu.cif.gz	175.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5vcu.ent.gz	136.2 KB	Display	PDB format
PDBx/mmJSON format	5vcu.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/vc/5vcu ftp://data.pdbj.org/pub/pdb/validation_reports/vc/5vcu	HTTPS FTP

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Related structure data

Related structure data	2qmeS S: Starting model for refinement
Similar structure data	5n1w-1 3su2-d 6pj1-d 6piw-d 2f9m-d 6dis-d 4g6t-d 5n1w-2 6piy-d 2hww-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: SSGCID-NafoA.00927.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#245 - May 2020 Spliceosomes similarity (2)

Deposited unit

A: Ras-related c3 botulinum toxin substrate 1 isoform x2

B: Ras-related c3 botulinum toxin substrate 1 isoform x2

hetero molecules

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

1

A: Ras-related c3 botulinum toxin substrate 1 isoform x2

hetero molecules

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

2

B: Ras-related c3 botulinum toxin substrate 1 isoform x2

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)	48.380, 48.380, 624.560
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-465- HOH
2	1	B-470- HOH
3	1	B-527- HOH

#1: Protein	Ras-related c3 botulinum toxin substrate 1 isoform x2 / NafoA.00927.a Mass: 23488.852 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba) Strain: ATCC 30863 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1Z0YU85*PLUS
#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: 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.: 397 / 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: 2.25 Å³/Da / Density % sol: 45.35 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MCSG1 B2 (287414b2): 25% PEG3350, 100mM Bis-Tris: HCl pH 5.5, 200mM NaCl, 4mM GTP, 4mM MgCl2, protein conc. 24mg/mL, cryo 15% ethylene glycol (2-step): puck id gcf4-5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2017 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.85→35.868 Å / Num. obs: 39544 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 19.972 % / B_iso Wilson estimate: 27.55 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.076 / R_rim(I) all: 0.078 / Χ²: 1.056 / Net I/σ(I): 26.17 / Num. measured all: 789781 / Scaling rejects: 2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.85-1.9	20.907	0.54	5.32	2800	0.988	0.554	100
1.9-1.95	21.107	0.426	6.9	2773	0.991	0.436	100
1.95-2.01	20.9	0.322	8.95	2708	0.993	0.33	100
2.01-2.07	21.052	0.25	11.92	2560	0.995	0.256	100
2.07-2.14	21.024	0.206	14.4	2551	0.996	0.211	100
2.14-2.21	20.735	0.174	17.42	2517	0.996	0.179	100
2.21-2.29	20.97	0.141	21.83	2353	0.997	0.145	100
2.29-2.39	20.595	0.131	23.15	2292	0.997	0.134	99.9
2.39-2.49	20.25	0.111	27.03	2212	0.997	0.114	100
2.49-2.62	20.131	0.098	30.32	2141	0.998	0.101	100
2.62-2.76	19.887	0.088	33.2	2019	0.998	0.09	100
2.76-2.93	19.597	0.08	37.21	1941	0.998	0.082	99.9
2.93-3.13	19.019	0.07	41.09	1854	0.998	0.072	100
3.13-3.38	18.801	0.063	45.72	1718	0.999	0.065	100
3.38-3.7	18.435	0.058	48.18	1625	0.998	0.06	100
3.7-4.14	18.341	0.055	49.49	1471	0.999	0.057	99.9
4.14-4.78	18.325	0.054	50.11	1327	0.999	0.056	99.9
4.78-5.85	18.352	0.051	49.06	1147	0.999	0.052	100
5.85-8.27	17.175	0.049	47.38	952	0.998	0.051	99.9
8.27-50	12.961	0.045	40.21	583	0.999	0.047	98

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	dev_2719	refinement
XSCALE		data scaling
Coot		model building
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2qme

2qme

Resolution: 1.85→35.868 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.72

	R_factor	Num. reflection	% reflection
R_free	0.2108	1979	5.01 %
R_work	0.1742	-	-
obs	0.176	39482	99.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 102.25 Å² / B_iso mean: 35.78 Å² / B_iso min: 17.45 Å²

Refinement step

Cycle: final / Resolution: 1.85→35.868 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2835	0	58	399	3292
B_iso mean	-	-	26.9	42.16	-
Num. residues	-	-	-	-	370

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3003
X-RAY DIFFRACTION	f_angle_d	0.935	4097
X-RAY DIFFRACTION	f_chiral_restr	0.061	462
X-RAY DIFFRACTION	f_plane_restr	0.006	522
X-RAY DIFFRACTION	f_dihedral_angle_d	15.641	1847

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8501-1.8964	0.3107	141	0.2349	2554	2695	100
1.8964-1.9476	0.2798	140	0.2049	2605	2745	100
1.9476-2.0049	0.2489	129	0.1926	2613	2742	100
2.0049-2.0696	0.2299	131	0.1925	2559	2690	100
2.0696-2.1436	0.2241	137	0.184	2601	2738	100
2.1436-2.2294	0.2134	156	0.1765	2630	2786	100
2.2294-2.3309	0.1928	131	0.1688	2647	2778	100
2.3309-2.4537	0.2333	140	0.17	2646	2786	100
2.4537-2.6074	0.1694	136	0.1763	2651	2787	100
2.6074-2.8087	0.2378	140	0.1873	2688	2828	100
2.8087-3.0912	0.2613	145	0.1914	2682	2827	100
3.0912-3.5381	0.1951	146	0.171	2756	2902	100
3.5381-4.4563	0.1818	139	0.149	2827	2966	100
4.4563-35.8746	0.1959	168	0.1717	3044	3212	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	0.2096	-0.2482	-0.8364	5.346	2.0111	3.5024	-0.0277	0.1727	-0.133	-0.3094	-0.1699	0.5519	-0.2174	-0.1676	0.1982	0.5294	0.2266	-0.0429	0.3935	0.0476	0.2712	-4.4259	-8.1279	-51.8897
2	1.8321	0.9618	-0.5409	3.1926	-0.6603	2.0755	0.1687	0.0007	0.1592	-0.1543	-0.2895	0.2097	-0.3274	0.0467	0.0752	0.3426	0.1017	0.0058	0.2226	0.0048	0.2294	0.9563	-13.6403	-41.8467
3	3.7289	2.9289	0.0074	4.7139	-2.7495	3.9182	0.3674	0.9129	-0.5504	-0.6175	-0.5714	0.1295	0.2768	-0.4169	0.3792	0.3994	0.1751	-0.0571	0.324	-0.093	0.2859	-1.4023	-24.4205	-47.0536
4	3.5235	3.9596	-1.5168	4.858	-3.0299	7.3151	0.1484	0.3472	-0.102	-0.3109	-0.199	-0.1995	-0.3358	0.4956	0.0822	0.3615	0.166	0.0488	0.2767	0.0209	0.2246	5.8506	-14.4975	-46.7258
5	4.1317	4.1394	3.0228	4.1591	3.1314	5.0543	0.166	-0.1221	-0.5859	0.6948	-0.1427	0.4895	0.5324	-0.5919	-0.0526	0.3173	0.0127	0.0343	0.2523	0.0136	0.4487	-14.1575	-29.2466	-33.4376
6	5.7096	5.7601	0.9218	6.4995	0.7676	0.6528	0.118	0.3448	-0.6141	-0.0936	-0.1177	-0.0263	0.0466	0.0285	-0.0035	0.3346	0.1372	-0.0544	0.2631	-0.0628	0.3391	0.2234	-29.6045	-39.2128
7	8.9686	2.3416	-3.7097	2.5847	-2.952	5.3764	0.1506	-0.4063	0.0511	0.0698	-0.0273	0.1074	-0.4148	-0.0494	-0.042	0.2945	0.0624	-0.0154	0.1294	-0.0244	0.1478	-1.121	-18.8478	-32.2423
8	2.3647	2.3284	0.939	6.6706	1.4018	4.0189	-0.1785	-0.142	-0.2479	-0.4848	-0.1343	-0.4952	-0.3696	0.463	0.2717	0.4596	0.034	0.0009	0.2141	0.0774	0.2356	9.5175	-9.9794	-32.1372
9	5.1612	-0.8677	-1.0802	6.3173	4.7277	3.8198	0.0242	0.6697	-0.5089	-0.1517	-0.2188	0.2132	0.1748	0.4471	0.0514	0.3023	0.1111	-0.0259	0.3072	-0.0199	0.2364	16.4705	-29.7459	-21.147
10	5.3097	-1.6155	4.2952	5.5198	2.6518	6.8603	0.2892	-0.5587	-0.8258	0.4336	-0.1119	0.2546	0.7071	-0.3527	-0.1188	0.3828	-0.0514	0.0452	0.2033	0.0547	0.3046	5.429	-28.9116	-9.5759
11	3.8293	-0.1603	3.0813	3.3968	-1.9421	3.4258	0.2983	0.0091	-0.2528	-0.1498	-0.1329	0.0564	0.9711	0.0853	-0.2725	0.3772	0.0828	-0.0132	0.24	-0.022	0.3078	10.9442	-32.7927	-25.2016
12	8.8355	6.6229	4.8457	8.3756	6.9084	6.5167	-0.2186	-0.1634	0.478	0.1337	-0.148	-0.0311	-0.3134	0.0055	0.3818	0.3229	0.0092	-0.0504	0.214	0.0547	0.2849	19.5275	-24.8074	-1.9261
13	5.1451	-2.5271	-0.4554	2.1458	0.4223	3.1144	0.0304	0.066	0.2649	0.1325	-0.0646	-0.2957	-0.2421	0.4262	0.02	0.2582	-0.0612	-0.0245	0.1689	0.0515	0.2368	18.2322	-17.9893	-12.0891
14	7.1399	-0.845	-1.8358	9.1422	6.5879	5.7294	0.0097	0.06	0.2417	0.2794	-0.1387	0.7484	-0.1738	-0.4067	0.099	0.3474	0.0504	0.04	0.157	0.0563	0.2108	-4.2541	-9.8747	-5.6674
15	4.8459	-2.9634	-4.3237	3.2205	1.7519	4.6724	0.3956	-0.046	0.7107	-0.1667	-0.0614	-0.1254	-0.8444	0.1086	-0.3615	0.4494	-0.0457	0.0057	0.1422	0.0027	0.2979	9.2033	-5.4399	-13.5831
16	2.2236	0.9607	-2.2384	0.9107	-1.1672	2.5504	0.175	0.0295	-0.1327	-0.1009	-0.1548	-0.1041	-0.1097	0.0178	-0.0533	0.2843	0.0166	0.0204	0.1532	-0.0026	0.2368	5.1669	-17.0094	-17.9556
17	4.5651	0.7869	-6.1578	3.6315	-0.2033	9.1671	-0.0671	0.2075	0.1939	0.0846	-0.001	-0.3437	0.0304	0.3573	0.0381	0.2344	0.0676	-0.0442	0.2381	0.021	0.248	15.4671	-23.5627	-28.6283
18	2.4538	0.3031	-0.0027	3.3606	0.0285	3.8906	0.032	0.114	0.1859	-0.0582	-0.1772	0.0646	-0.9072	-0.0792	0.1497	0.4623	0.0982	-0.0092	0.1952	0.0328	0.2094	-1.8203	-7.6018	-36.591
19	3.8448	3.4331	-0.9453	5.2923	-4.5423	6.4326	-0.6687	0.5802	0.263	-0.8383	1.0197	0.8997	0.0006	-0.5287	-0.2769	0.7446	0.1141	-0.0186	0.5485	-0.0201	0.5552	-13.8836	-7.1206	-36.7157
20	6.0278	-0.1227	3.5671	3.8246	-1.4481	6.8932	-0.279	-0.0006	0.7275	-0.1409	-0.2539	0.1643	-0.994	-0.4658	0.5187	0.6894	0.1091	-0.0252	0.2404	0.0239	0.2841	3.6204	-1.8476	-30.6691

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 57 through 71 )	B	57 - 71
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 72 through 86 )	B	72 - 86
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 87 through 95 )	B	87 - 95
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 96 through 115 )	B	96 - 115
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 116 through 132 )	B	116 - 132
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 133 through 148 )	B	133 - 148
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 149 through 164 )	B	149 - 164
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 165 through 183 )	B	165 - 183
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1 through 10 )	A	1 - 10
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 11 through 39 )	A	11 - 39
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 40 through 56 )	A	40 - 56
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 57 through 67 )	A	57 - 67
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 68 through 115 )	A	68 - 115
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 116 through 132 )	A	116 - 132
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 133 through 148 )	A	133 - 148
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 149 through 164 )	A	149 - 164
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 165 through 186 )	A	165 - 186
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 0 through 25 )	B	0 - 25
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 26 through 38 )	B	26 - 38
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 39 through 56 )	B	39 - 56

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+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi