PDB-5k8s: cAMP bound PfPKA-R (297-441)

ID or keywords:

Entry

Database: PDB / ID: 5k8s

Title

cAMP bound PfPKA-R (297-441)

Components

CAMP-dependent protein kinase regulatory subunit

Keywords

TRANSFERASE / Plasmodium falciparum / PKA / protein kinase A / cAMP / CBD / cyclic nucleotide binding / CNB / regulatory domain / R

Function / homology

Function and homology information

cAMP-dependent protein kinase regulator activity / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding / cAMP binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein-containing complex / cytosol
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.15 Å

Authors

Littler, D.R. / Gilson, P.R. / Crabb, B.S. / Rossjohn, J.J.

Citation

Journal: J. Biol. Chem. / Year: 2016
Title: Disrupting the Allosteric Interaction between the Plasmodium falciparum cAMP-dependent Kinase and Its Regulatory Subunit.
Authors: Littler, D.R. / Bullen, H.E. / Harvey, K.L. / Beddoe, T. / Crabb, B.S. / Rossjohn, J. / Gilson, P.R.

History

Deposition	May 31, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 26, 2016	Group: Database references
Revision 1.2	Dec 14, 2016	Group: Database references
Revision 1.3	Feb 26, 2020	Group: Data collection / Category: diffrn_source / reflns Item: _diffrn_source.pdbx_synchrotron_site / _reflns.pdbx_Rmerge_I_obs
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5k8s.cif.gz	148.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5k8s.ent.gz	116 KB	Display	PDB format
PDBx/mmJSON format	5k8s.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5k8s_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	5k8s_full_validation.pdf.gz	1 MB	Display
Data in XML	5k8s_validation.xml.gz	18.1 KB	Display
Data in CIF	5k8s_validation.cif.gz	26.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k8/5k8s ftp://data.pdbj.org/pub/pdb/validation_reports/k8/5k8s	HTTPS FTP

-
Related structure data

Related structure data	5kbfC 5t3nC 1rgsS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4kz1-d 1py2-5 1py2-3 1y2f-d 3ogj-4 4zf7-1 4ijh-d 6dx1-1 4mei-d 4lso-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
Related items in Molecule of the Month	#152 - Aug 2012 cAMP-dependent Protein Kinase similarity (11) #48 - Dec 2003 Catabolite Activator Protein similarity (9) #251 - Nov 2020 Adenylyl Cyclase similarity (8) #183 - Mar 2015 Phototropin similarity (1)

Deposited unit

A: CAMP-dependent protein kinase regulatory subunit

B: CAMP-dependent protein kinase regulatory subunit

hetero molecules

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

1

A: CAMP-dependent protein kinase regulatory subunit

hetero molecules

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

2

B: CAMP-dependent protein kinase regulatory subunit

hetero molecules

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

Unit cell

Length a, b, c (Å)	39.280, 71.820, 106.470
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	CAMP-dependent protein kinase regulatory subunit Mass: 16863.379 Da / Num. of mol.: 2 / Fragment: UNP residues 297-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PKAr, PFL1110c / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7KQK0
#2: Chemical	ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₂N₅O₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.75 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 22% w/v Polyethylene glycol 6000, 0.1M LiCl and 0.1M CH3COONa pH 4

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.15→42.8 Å / Num. obs: 104403 / % possible obs: 97.2 % / Redundancy: 7.9 % / R_merge(I) obs: 0.041 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.15→1.21 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / % possible all: 89.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.8.4_1496	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1RGS

1rgs

Resolution: 1.15→34.027 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.24

	R_factor	Num. reflection	% reflection
R_free	0.2183	5163	4.95 %
R_work	0.1975	-	-
obs	0.1985	104241	96.79 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.15→34.027 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2345	0	44	355	2744

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	2578
X-RAY DIFFRACTION	f_angle_d	1.311	3508
X-RAY DIFFRACTION	f_dihedral_angle_d	15.126	1042
X-RAY DIFFRACTION	f_chiral_restr	0.052	395
X-RAY DIFFRACTION	f_plane_restr	0.006	446

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 (%)
1.15-1.1631	0.3322	138	0.2904	2659	X-RAY DIFFRACTION	79
1.1631-1.1768	0.286	159	0.2813	2894	X-RAY DIFFRACTION	86
1.1768-1.1911	0.2771	155	0.275	3079	X-RAY DIFFRACTION	90
1.1911-1.2062	0.2523	172	0.2717	3173	X-RAY DIFFRACTION	95
1.2062-1.2221	0.3448	184	0.3109	3389	X-RAY DIFFRACTION	99
1.2221-1.2388	0.3187	178	0.2969	3325	X-RAY DIFFRACTION	99
1.2388-1.2565	0.2586	163	0.2326	3345	X-RAY DIFFRACTION	100
1.2565-1.2753	0.2499	176	0.2305	3398	X-RAY DIFFRACTION	100
1.2753-1.2952	0.2622	181	0.2562	3313	X-RAY DIFFRACTION	100
1.2952-1.3164	0.3316	189	0.3112	3367	X-RAY DIFFRACTION	99
1.3164-1.3391	0.2259	169	0.2086	3373	X-RAY DIFFRACTION	100
1.3391-1.3635	0.2174	202	0.2026	3369	X-RAY DIFFRACTION	100
1.3635-1.3897	0.2398	175	0.2012	3362	X-RAY DIFFRACTION	100
1.3897-1.4181	0.2107	170	0.195	3420	X-RAY DIFFRACTION	100
1.4181-1.4489	0.2104	172	0.1991	3382	X-RAY DIFFRACTION	100
1.4489-1.4826	0.2361	164	0.207	3379	X-RAY DIFFRACTION	100
1.4826-1.5197	0.1895	157	0.1876	3445	X-RAY DIFFRACTION	100
1.5197-1.5608	0.2149	179	0.1888	3396	X-RAY DIFFRACTION	100
1.5608-1.6067	0.1865	205	0.1809	3355	X-RAY DIFFRACTION	100
1.6067-1.6585	0.214	177	0.183	3407	X-RAY DIFFRACTION	100
1.6585-1.7178	0.2228	165	0.1877	3420	X-RAY DIFFRACTION	100
1.7178-1.7866	0.2034	177	0.1887	3409	X-RAY DIFFRACTION	100
1.7866-1.8679	0.2162	187	0.1848	3409	X-RAY DIFFRACTION	100
1.8679-1.9664	0.2653	148	0.2146	3393	X-RAY DIFFRACTION	99
1.9664-2.0896	0.1717	163	0.1732	3428	X-RAY DIFFRACTION	99
2.0896-2.2509	0.1892	182	0.1853	3391	X-RAY DIFFRACTION	99
2.2509-2.4773	0.2002	177	0.1848	3446	X-RAY DIFFRACTION	99
2.4773-2.8356	0.214	203	0.1853	3419	X-RAY DIFFRACTION	99
2.8356-3.572	0.1929	174	0.1779	3405	X-RAY DIFFRACTION	96
3.572-34.0416	0.2453	122	0.198	2528	X-RAY DIFFRACTION	69

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	5.1677	-0.5857	2.0839	4.6489	0.5132	5.0518	0.1381	-0.1728	-0.0404	0.0181	-0.0196	0.3798	-0.0945	-0.5328	-0.1457	0.1195	0.0144	0.0492	0.2212	0.0037	0.1666	0.725	-7.52	-14.2897
2	1.0538	-0.1324	0.584	2.3218	0.9053	1.3942	0.1021	-0.0354	0.1187	-0.2629	-0.1075	-0.126	-0.1219	-0.0349	0.0009	0.1021	-0.0054	0.0469	0.1312	0.0298	0.0912	9.296	-13.1226	-22.146
3	1.9756	-0.5449	0.7967	3.8239	-1.0884	2.0948	0.1254	-0.0747	-0.0758	0.0556	-0.1372	-0.2097	0.0108	0.0621	-0.0069	0.079	-0.0084	-0.0036	0.101	0.0138	0.0659	12.6847	-24.6775	-16.2019
4	3.396	0.0321	-1.0382	3.9105	0.254	3.6575	0.1591	-0.0734	0.1986	0.0743	-0.1017	-0.3154	-0.2137	0.128	-0.0355	0.1082	-0.0131	-0.0066	0.0826	0.0185	0.0981	16.543	-16.5676	-16.3903
5	1.1522	0.2543	0.6398	3.9569	0.9456	1.0632	0.0533	0.0271	0.0704	-0.1972	-0.0193	-0.1575	-0.1398	0.0322	-0.027	0.1341	0.007	0.0369	0.1372	0.0183	0.0829	10.6223	-14.8069	-21.4574
6	5.4469	-4.4898	1.5105	3.6912	-1.2337	1.211	-0.0102	-0.3139	0.0102	0.4207	0.0157	-0.3119	-0.1355	-0.0938	0.0228	0.1908	-0.0344	-0.0431	0.1549	0.019	0.1347	19.2011	-15.2249	-6.5534
7	5.5602	-0.8497	-2.8855	7.0864	-2.789	4.9585	0.1446	-0.181	-0.0848	-0.05	-0.2651	-1.403	-0.2968	0.3462	0.1842	0.1549	-0.0626	-0.1079	0.2102	0.0823	0.3041	27.4098	-22.9828	-10.5111
8	5.2663	-1.6881	1.5079	2.2441	-2.3948	5.5891	-0.0585	0.0369	0.2527	-0.0229	-0.1749	-0.0741	0.1267	0.6697	0.1933	0.1458	0.0004	-0.0119	0.1881	0.0075	0.0863	15.5383	-42.6401	16.0802
9	9.5769	3.2244	-6.7209	6.2033	-3.5785	9.306	-0.3714	-0.1301	0.4118	0.6166	0.5068	0.4847	-0.245	-0.324	-0.1336	0.2836	0.0585	-0.0261	0.195	0.0383	0.2602	4.2356	-35.4548	12.3778
10	4.6805	-0.6325	-4.7486	1.2435	0.0618	8.0796	-0.0561	-0.0604	0.0995	0.126	0.0204	-0.0061	0.0791	-0.0879	0.0632	0.0949	-0.0033	-0.0153	0.1001	0.0076	0.1071	10.5807	-45.7533	12.254
11	4.8287	0.7356	1.1912	2.6019	0.3331	3.9163	-0.0277	0.2555	-0.3189	-0.0459	-0.1208	-0.1737	0.2892	0.0806	0.1549	0.1217	0.002	0.0166	0.0837	-0.0036	0.1283	12.6055	-47.7364	-8.3025
12	2.0267	0.0424	0.5501	1.8671	-1.7317	3.9675	-0.0464	0.1037	-0.0166	-0.0451	0.0057	-0.0338	-0.0233	0.071	0.0467	0.1046	0.0013	-0.0243	0.0758	-0.0012	0.1002	10.6055	-38.8085	-6.2772
13	9.6143	5.8362	-1.1501	3.6724	-0.4777	2.7043	-0.0532	-0.1217	0.5302	0.1148	-0.0167	0.3694	-0.1952	-0.0331	0.0253	0.1339	0.0168	-0.0284	0.0925	0.0138	0.1029	8.6244	-37.5323	0.3359
14	5.6571	1.4751	0.5637	1.6422	-0.4333	2.1515	-0.0851	0.1454	-0.0587	-0.0281	0.0347	0.0074	0.0324	-0.0414	0.048	0.0933	0.0024	-0.0042	0.0502	-0.0097	0.0891	7.6047	-44.5128	-6.2923
15	4.7761	0.5341	-1.7519	1.2121	-0.4791	2.8281	-0.1029	-0.1195	-0.2568	-0.0389	0.0099	0.0989	0.2248	-0.1017	0.0985	0.1392	0.0066	-0.0198	0.0969	0.0188	0.1154	6.3993	-48.3293	6.4619
16	2.1938	0.3738	-1.3104	1.2496	-0.8554	8.4927	-0.1808	-0.0265	0.1346	0.082	-0.016	0.0986	-0.1956	-0.4364	0.1423	0.1086	0.019	-0.013	0.1171	-0.0156	0.1402	-3.3853	-36.1823	-3.2174
17	8.5159	6.7228	-4.9663	8.713	-5.7235	7.2408	-0.4215	0.3242	-0.1555	-0.3094	0.4434	0.2459	0.6455	-0.6399	-0.1149	0.1654	-0.0556	-0.0113	0.1872	0.0175	0.1991	-4.4466	-42.9726	-12.8427

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 297 through 317 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 318 through 347 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 348 through 369 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 370 through 388 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 389 through 410 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 411 through 430 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 431 through 439 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 294 through 309 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 310 through 317 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 318 through 333 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 334 through 347 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 348 through 369 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 370 through 377 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 378 through 395 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 396 through 410 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 411 through 430 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 431 through 441 )

-
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