PDB-5ck4: Signal recognition particle receptor SRb-GDP from Chaetomium ther...

ID or keywords:

Entry

Database: PDB / ID: 5ck4

Title

Signal recognition particle receptor SRb-GDP 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: 1.89 Å

Authors

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

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	May 8, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ck4.cif.gz	196.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ck4.ent.gz	155.5 KB	Display	PDB format
PDBx/mmJSON format	5ck4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ck4_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	5ck4_full_validation.pdf.gz	1.2 MB	Display
Data in XML	5ck4_validation.xml.gz	22 KB	Display
Data in CIF	5ck4_validation.cif.gz	32.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ck/5ck4 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/5ck4	HTTPS FTP

-
Related structure data

Related structure data	5ck3C 5ck5C C: citing same article (ref.)
Similar structure data	3w8s-d 3m3m-d 1rxh-d 5cse-d 6avk-d 5wxx-d 4uc7-1 1lcz-d 6uky-d 2iyu-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative signal recognition particle protein

B: Putative signal recognition particle protein

hetero molecules

69.8 kDa, 2 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)

Unit cell

Length a, b, c (Å)	34.960, 64.310, 64.930
Angle α, β, γ (deg.)	86.46, 90.13, 79.58
Int Tables number	1
Space group name H-M	P1

#1: Protein	Putative signal recognition particle protein Mass: 34438.000 Da / Num. of mol.: 2 / Fragment: resdieus 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.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.88 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium acetate, 20% (w/v) PEG3350

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.99 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99 Å / Relative weight: 1
Reflection	Resolution: 1.89→34.38 Å / Num. obs: 44352 / % possible obs: 97.65 % / Redundancy: 2.5 % / R_merge(I) obs: 0.062 / Net I/σ(I): 9.4

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.89→34.38 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 20.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2045	2211	5.08 %
R_work	0.1651	-	-
obs	0.1671	43483	97.65 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.89→34.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3347	0	56	410	3813

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3497
X-RAY DIFFRACTION	f_angle_d	1.046	4745
X-RAY DIFFRACTION	f_dihedral_angle_d	12.396	1301
X-RAY DIFFRACTION	f_chiral_restr	0.067	540
X-RAY DIFFRACTION	f_plane_restr	0.004	587

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 (%)
1.889-1.9301	0.2743	143	0.2393	2489	X-RAY DIFFRACTION	94
1.9301-1.975	0.2319	125	0.2098	2549	X-RAY DIFFRACTION	97
1.975-2.0243	0.2397	141	0.1927	2570	X-RAY DIFFRACTION	97
2.0243-2.0791	0.2216	137	0.1937	2561	X-RAY DIFFRACTION	97
2.0791-2.1402	0.2541	139	0.1809	2554	X-RAY DIFFRACTION	97
2.1402-2.2093	0.2072	140	0.1722	2612	X-RAY DIFFRACTION	98
2.2093-2.2883	0.2067	143	0.1723	2531	X-RAY DIFFRACTION	98
2.2883-2.3799	0.2141	133	0.1659	2624	X-RAY DIFFRACTION	98
2.3799-2.4881	0.2082	132	0.1634	2595	X-RAY DIFFRACTION	98
2.4881-2.6193	0.2175	135	0.1699	2565	X-RAY DIFFRACTION	98
2.6193-2.7833	0.2175	158	0.1688	2561	X-RAY DIFFRACTION	98
2.7833-2.9981	0.2476	137	0.1734	2588	X-RAY DIFFRACTION	98
2.9981-3.2996	0.2021	146	0.1615	2602	X-RAY DIFFRACTION	98
3.2996-3.7765	0.1677	126	0.1474	2644	X-RAY DIFFRACTION	99
3.7765-4.756	0.1612	144	0.1327	2597	X-RAY DIFFRACTION	99
4.756-34.3859	0.1996	132	0.1704	2630	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	3.2859	-0.3995	-0.1918	5.5593	0.7355	2.8498	-0.0084	0.542	-0.3427	-0.5317	0.121	0.5979	0.3782	-0.3913	0.0017	0.2287	-0.0503	-0.0472	0.2744	-0.0361	0.2009	-2.9976	12.6711	-18.1068
2	6.1502	-1.5263	-2.6592	5.042	1.1163	5.5816	0.1803	1.1518	-0.5979	-1.1121	-0.084	0.5162	0.8899	-0.5942	0.1019	0.5688	-0.0699	-0.1119	0.4834	-0.114	0.3204	-4.9742	8.5861	-20.9592
3	3.1381	0.2168	-0.2231	2.4404	-1.7338	2.9703	0.12	0.4555	-0.8537	-0.5095	-0.0946	0.3713	0.6634	-0.4445	-0.1111	0.3002	-0.0909	-0.0588	0.32	-0.0613	0.4572	-5.5272	3.3622	-8.7931
4	5.0096	0.3586	-0.0701	1.2156	-2.0968	3.6736	0.1523	-0.0073	0.0103	0.191	-0.076	0.1155	0.0268	-0.2392	0.0686	0.0979	0.0074	0.0077	0.1887	-0.0121	0.0684	1.1682	17.4196	-9.5722
5	2.1755	-0.2549	0.269	3.2099	-2.1126	3.5155	0.0163	-0.0844	-0.2062	0.0196	0.0086	-0.0084	0.0947	-0.1319	-0.0222	0.1034	-0.0203	0.0203	0.1266	-0.0163	0.1112	5.0072	12.6875	-5.141
6	2.9555	-0.2047	0.5409	4.037	-0.5195	5.8187	-0.072	-0.2293	-0.0263	0.2933	0.0029	-0.2226	0.0243	-0.067	0.0678	0.0882	-0.0263	0.0075	0.1261	-0.0216	0.1408	11.5512	15.6594	1.2605
7	4.8738	-3.9015	1.0568	6.5778	-1.0842	1.316	0.1264	0.7297	-0.037	-0.5688	-0.272	-0.3114	0.4415	0.3893	0.1491	0.3102	0.0576	0.0713	0.3607	-0.0101	0.1633	7.5616	18.0145	-20.9426
8	1.6647	1.2273	-0.7832	4.0853	-1.6854	3.0123	-0.0159	0.2051	0.3804	-0.054	-0.0532	-0.3464	-0.3605	0.1504	0.0955	0.1785	-0.0359	0.0029	0.1544	0.0351	0.216	19.9721	47.6333	13.1565
9	7.3464	2.3455	-0.6415	3.9827	-0.4984	3.6369	-0.0136	0.6169	0.3129	-0.9256	0.0879	-0.6267	-0.3179	0.1307	-0.1309	0.2812	0.0002	0.0587	0.288	0.0092	0.2635	23.2838	40.9159	8.2537
10	3.2668	-0.2527	-0.1246	3.2141	-0.6703	2.6682	0.0945	-0.005	0.3774	-0.2789	0.0131	-0.0865	-0.2327	0.0643	-0.0991	0.1783	-0.0715	0.0077	0.1582	0.0271	0.2439	20.1793	46.0577	17.7856
11	2.5882	1.8803	-1.1203	4.182	-1.9228	3.9376	0.1274	0.2893	0.4745	-0.3326	-0.1842	-0.2982	-0.4447	0.3371	-0.0093	0.2511	-0.0208	0.0351	0.2297	0.0829	0.27	19.9965	48.4634	13.3953
12	4.1834	0.5748	-0.5585	2.3103	1.2974	3.1936	-0.0854	-0.4458	-0.0266	0.5627	0.2077	-0.3027	0.2496	0.2956	-0.0754	0.1493	-0.0051	-0.0335	0.1963	0.0104	0.1037	14.818	37.518	30.0033
13	3.7241	-0.4882	-0.1061	2.3896	0.5038	3.8057	0.0459	0.0384	0.0923	-0.0143	-0.0028	0.2796	-0.0715	-0.2194	0.0164	0.0942	-0.0272	0.0134	0.1342	0.0204	0.0956	10.6069	35.7798	20.4439
14	4.2194	-0.1093	0.0811	6.0546	3.6087	2.3802	-0.1152	-0.3624	0.0322	0.5699	0.1268	-0.0164	0.3853	0.1827	-0.1775	0.1915	-0.0168	0.003	0.2038	0.0692	0.1353	8.3995	35.6925	35.9708
15	5.5473	0.9052	1.6165	5.0989	1.7929	2.6383	0.148	-0.725	0.4615	0.7787	0.1942	0.3602	-0.2518	-0.411	0.2482	0.2725	0.0081	0.0597	0.2621	-0.0274	0.2272	3.9505	43.5563	37.7264
16	3.3145	-2.7565	-2.6519	5.5014	4.6052	4.8652	0.1143	0.213	0.0977	-0.2751	-0.0936	0.0888	-0.1463	-0.2971	0.0186	0.1327	-0.0319	-0.0331	0.1847	0.0542	0.174	6.3704	37.5456	20.2265
17	4.7387	-4.6992	-1.6672	4.6927	1.7131	1.8541	0.1415	0.4247	0.0184	-0.6475	0.0628	0.388	-0.1315	-1.0547	-0.1508	0.3053	0.0198	-0.0878	0.3755	0.0549	0.2467	7.2071	39.0712	10.6252

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 48 through 71 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 72 through 150 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 151 through 189 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 190 through 210 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 211 through 259 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 260 through 326 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 327 through 347 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 45 through 62 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 63 through 134 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 135 through 166 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 167 through 201 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 202 through 231 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 232 through 259 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 260 through 282 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 283 through 311 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 312 through 336 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 337 through 347 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-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

-
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