PDB-5ck5: Signal recognition particle receptor SRb-GDP-Mg from Chaetomium t...

ID or keywords:

Entry

Database: PDB / ID: 5ck5

Title

Signal recognition particle receptor SRb-GDP-Mg from Chaetomium thermophilum

Components

Putative signal recognition particle protein

Keywords

SIGNALING PROTEIN / Arf-like GTPase / protein translocation

Function / homology

Function and homology information

endoplasmic reticulum membrane / GTP binding / metal ion binding
Similarity search - Function

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Jadhav, B.R. / Wild, K. / Sinning, I.

Citation

Journal: Structure / Year: 2015
Title: Structure and Switch Cycle of SR beta as Ancestral Eukaryotic GTPase Associated with Secretory Membranes.
Authors: Jadhav, B. / Wild, K. / Pool, M.R. / Sinning, I.

History

Deposition	Jul 15, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 9, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 14, 2015	Group: Database references
Revision 1.2	Jan 10, 2024	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_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5ck5.cif.gz	357.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5ck5.ent.gz	292 KB	Display	PDB format
PDBx/mmJSON format	5ck5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ck5_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	5ck5_full_validation.pdf.gz	1.8 MB	Display
Data in XML	5ck5_validation.xml.gz	34.2 KB	Display
Data in CIF	5ck5_validation.cif.gz	46 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ck/5ck5 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/5ck5	HTTPS FTP

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Related structure data

Related structure data	5ck3C 5ck4SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4u8e-d 4ucd-1 4uc6-2 4uc8-1 6t3z-d 6qp0-d 3c1u-d 5ck4-2 4l8e-d 4uc9-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5ck3C

5ck4SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative signal recognition particle protein

B: Putative signal recognition particle protein

C: Putative signal recognition particle protein

D: Putative signal recognition particle protein

hetero molecules

140 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative signal recognition particle protein

hetero molecules

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

2

B: Putative signal recognition particle protein

hetero molecules

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

3

C: Putative signal recognition particle protein

hetero molecules

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

4

D: Putative signal recognition particle protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.100, 137.970, 64.310
Angle α, β, γ (deg.)	90.00, 93.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative signal recognition particle protein Mass: 34438.000 Da / Num. of mol.: 4 / Fragment: residues 42-346 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0022040 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S401
#2: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.54 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M calcium acetate, 40% (w/v) PEG600, 0.1 M sodium cacodylate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.99 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 18, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 2.4→64.2 Å / Num. obs: 44980 / % possible obs: 99.5 % / Redundancy: 2 % / R_merge(I) obs: 0.065 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.4→2.5 Å / Redundancy: 2 % / R_merge(I) obs: 0.31 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
SCALA		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5ck4

5ck4

Resolution: 2.4→64.2 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 44.31 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2226	2163	5.06 %
R_work	0.1856	-	-
obs	0.1909	42718	95.18 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.4→64.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6679	0	116	92	6887

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6928
X-RAY DIFFRACTION	f_angle_d	1.408	9383
X-RAY DIFFRACTION	f_dihedral_angle_d	15.391	2561
X-RAY DIFFRACTION	f_chiral_restr	0.058	1067
X-RAY DIFFRACTION	f_plane_restr	0.007	1158

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 (%)
2.376-2.4313	0.3637	140	0.4026	2767	X-RAY DIFFRACTION	95
2.4313-2.4921	0.4625	163	0.3788	2849	X-RAY DIFFRACTION	94
2.4921-2.5595	0.4113	139	0.3365	2832	X-RAY DIFFRACTION	95
2.5595-2.6348	0.3997	145	0.3391	2800	X-RAY DIFFRACTION	95
2.6348-2.7198	0.4683	115	0.4246	2160	X-RAY DIFFRACTION	72
2.7198-2.817	0.2807	157	0.2862	2869	X-RAY DIFFRACTION	95
2.817-2.9298	0.2924	149	0.2532	2827	X-RAY DIFFRACTION	95
2.9298-3.0631	0.2541	161	0.2257	2799	X-RAY DIFFRACTION	94
3.0631-3.2246	0.2208	155	0.2063	2828	X-RAY DIFFRACTION	95
3.2246-3.4265	0.2333	140	0.1982	2822	X-RAY DIFFRACTION	95
3.4265-3.691	0.195	101	0.171	2114	X-RAY DIFFRACTION	71
3.691-4.0622	0.2048	136	0.1501	2507	X-RAY DIFFRACTION	83
4.0622-4.6496	0.1631	151	0.109	2836	X-RAY DIFFRACTION	95
4.6496-5.8563	0.1883	135	0.1198	2859	X-RAY DIFFRACTION	95
5.8563-47.0118	0.1612	152	0.1267	2708	X-RAY DIFFRACTION	89

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	6.2511	0.8126	0.5307	3.0427	-1.8073	3.5073	-0.1705	0.9436	-0.2428	-0.4233	-0.0966	-0.4735	0.2386	0.7909	0.116	0.5022	0.001	0.0657	0.2933	-0.1078	0.4294	6.6767	-39.5643	-71.8085
2	2.1153	0.3742	0.5762	3.1505	1.1508	1.6997	0.1701	0.2571	-0.4284	0.0114	0.0043	-0.22	0.156	0.3523	-0.0615	0.3732	0.0323	-0.0134	0.1494	-0.0001	0.3319	5.5976	-37.1169	-57.9721
3	1.6902	-0.3888	1.2984	1.0677	-0.5855	3.909	-0.0467	0.8118	0.3362	-0.0884	0.1534	-0.0415	-0.2045	0.3209	-0.0434	0.3836	-0.011	0.0163	0.0717	0.0226	0.248	1.7238	-29.5102	-60.8397
4	2.5307	0.2072	1.0403	2.3603	0.4756	4.3788	-0.0197	-0.0106	0.5397	0.0892	-0.1098	-0.0378	-0.3123	0.0749	0.0626	0.3248	0.0268	0.029	0.116	0.0007	0.3336	-2.7996	-26.2471	-52.6062
5	8.9886	2.4254	-2.1219	6.8989	2.1586	2.7712	-0.3598	1.2212	0.0651	-1.3936	-0.1177	-0.6475	-0.7453	0.3943	0.4533	0.4239	-0.03	0.0009	0.547	0.1992	0.3525	0.7966	-27.0819	-71.6574
6	1.6329	1.5935	0.9872	4.644	-1.8569	4.1904	0.1265	-0.1118	-0.1819	-0.2142	0.373	0.5054	-0.0152	-0.5632	0.6282	0.4119	0.0899	-0.0152	0.1016	-0.1056	0.2465	-34.233	-22.1026	-38.207
7	4.6685	0.2837	-1.4779	0.3575	-0.1116	0.8433	-0.2591	1.0915	0.9526	-0.4315	0.1321	0.0984	-0.0197	-0.4463	0.033	0.4857	-0.0093	-0.0178	0.3027	0.1408	0.3507	-28.7228	-17.4834	-42.8855
8	2.3394	-1.4734	-1.15	1.7359	-0.6812	3.1664	0.1118	0.1487	-0.0095	0.2371	0.1067	0.2222	-0.1497	-0.1291	-0.2772	0.2902	-0.0319	-0.0399	0.0851	-0.0824	0.4101	-31.6391	-20.6582	-33.8888
9	7.2148	1.7165	-2.4342	6.8279	-1.4667	6.8092	-0.3731	0.7915	0.0669	-0.8705	0.6595	0.53	-0.4891	-0.8779	-0.3791	0.5254	-0.1903	-0.0874	0.5954	0.0705	0.3608	-41.8412	-19.5755	-39.4386
10	1.9294	-0.5249	-0.2237	1.912	-0.1189	1.1373	-0.1134	-0.3461	0.0172	-0.0151	0.003	0.0184	0.1347	0.0588	-0.0142	0.4029	-0.0333	-0.0361	0.0157	0.0215	0.2522	-26.1462	-25.4986	-25.8736
11	1.5494	0.2095	-0.1657	1.6183	-0.0889	2.408	-0.1208	0.0188	-0.2246	-0.024	-0.0391	-0.0615	0.207	-0.0704	0.0479	0.3498	0.0914	-0.0708	0.2361	-0.1064	0.3501	-22.709	-29.6139	-30.7138
12	2.3774	0.3112	-1.3987	2.8392	-0.1324	6.4899	0.199	-0.189	0.294	0.3581	0.1654	-0.1921	-0.1893	0.15	-0.0637	0.3113	0.0229	-0.1061	0.2379	-0.049	0.3046	-19.6994	-31.6986	-17.0734
13	0.9252	0.2183	-0.264	0.8561	-0.2986	1.8658	0.0542	-0.1102	-0.3005	0.0848	0.1123	-0.0145	0.3525	-0.242	-0.0934	0.5351	0.0238	-0.0858	0.0976	0.0197	0.4857	-24.3664	-34.5319	-23.6624
14	6.2217	4.3316	1.9426	7.9355	-0.0528	3.9475	0.4008	0.9316	-0.5584	-0.1826	-0.2605	-0.6521	0.6484	0.0202	-0.1189	0.3988	0.0051	0.1048	0.2157	-0.1561	0.5104	-23.6629	-32.9025	-41.0998
15	2.5523	-0.0112	0.8549	1.7835	-1.4542	5.4898	0.146	0.6549	-0.4623	-0.3922	-0.1033	0.9997	-0.0257	0.3596	0.0363	0.6556	-0.1674	-0.0983	0.3309	-0.0314	0.5738	-15.9352	-4.0668	0.6307
16	1.1638	-1.4354	0.7477	5.0638	1.5018	2.2657	-0.4757	0.449	-1.4619	-0.6377	0.3644	0.9345	0.9668	-0.4901	0.2082	0.7834	-0.156	-0.0405	0.4388	-0	0.8655	-21.694	-5.0437	-4.9438
17	5.8477	-2.4399	0.2474	4.0078	-0.1857	2.2749	0.2523	-0.1088	-0.3748	-0.798	0.1307	-0.3166	0.4018	0.2168	-0.2026	0.6222	-0.0153	0.0515	0.2368	-0.0546	0.6655	-6.9749	-4.712	-4.5522
18	3.0175	-0.142	-0.7722	2.3168	1.0086	0.6056	-0.1481	0.1869	-0.1684	-0.4194	0.131	0.1433	0.1644	-0.0534	-0.0778	0.4336	-0.0478	-0.0177	0.2203	0.0336	0.3692	-4.9247	-0.091	-1.4262
19	2.2008	-0.8402	0.1473	2.2581	-0.3829	1.2189	0.1073	0.3185	0.4064	-0.8459	-0.1631	-0.2143	-0.1082	0.0531	-0.1513	0.7343	-0.044	-0.0902	0.3238	0.2778	0.6254	-1.6229	13.7766	-14.7847
20	2.8869	0.9896	-0.1757	1.5746	-0.3967	1.2694	-0.1163	0.2538	0.1188	-0.1948	-0.0793	0.0748	-0.0102	0.0149	0.173	0.3586	-0.0086	-0.0779	0.1948	0.0616	0.347	-3.9468	7.3992	7.6619
21	2.3499	-1.1222	1.9259	4.4892	1.9891	3.7247	-0.2323	0.4263	0.8219	-0.9584	-0.0685	-0.3695	-0.8697	0.7404	0.0646	0.7838	-0.3458	0.0277	0.3674	0.0386	0.6921	-15.1763	-54.7041	-31.2486
22	3.1033	-2.2395	1.7419	1.674	-1.035	2.6022	-0.0294	0.086	0.3242	-0.2206	-0.1078	-0.4349	-0.0577	1.4109	-0.0054	0.4661	-0.1894	0.0678	0.8181	0.0609	0.8077	-9.0779	-61.0686	-32.6842
23	1.2185	1.1269	0.6046	2.8459	0.284	1.1364	-0.4862	0.3709	0.4316	-0.6406	0.2191	-0.1643	-0.3863	0.1641	0.0135	0.8918	-0.233	-0.0349	0.3385	0.225	0.9123	-24.2347	-55.7738	-38.6804
24	3.1593	0.6756	1.3332	3.2388	-0.6109	1.7136	-0.3825	0.0076	0.5197	0.01	0.1303	0.3249	-0.7355	-0.5203	0.1873	0.4295	-0.0012	-0.0307	0.19	-0.0303	0.5559	-27.2766	-59.2099	-21.205
25	1.9981	1.2189	0.7762	1.945	0.3668	1.0935	-0.2589	-0.1356	0.3129	-0.1917	-0.0689	0.1721	-0.1293	-0.2394	0.1839	0.512	0.0143	-0.089	0.0379	-0.0675	0.5177	-31.5234	-66.5264	-25.1176
26	2.9063	0.4546	0.499	5.4076	4.7138	5.18	-0.2112	0.2772	-0.2882	0.0664	0.285	-0.6185	0.2195	0.5036	0.1052	0.3403	0.051	0.0793	0.447	-0.1295	0.5595	-14.1402	-68.4815	-25.6576

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 47 through 145 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 146 through 232 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 233 through 259 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 260 through 336 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 337 through 347 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 45 through 62 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 63 through 134 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 135 through 162 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 163 through 188 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 189 through 231 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 232 through 259 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 260 through 279 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 280 through 336 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 337 through 347 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 48 through 72 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 73 through 140 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 141 through 162 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 163 through 231 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 232 through 243 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 244 through 347 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 50 through 134 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 135 through 145 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 146 through 192 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 193 through 210 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 211 through 336 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 337 through 347 )

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-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

-
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