PDB-6dfk: Crystal structure of the 11S subunit of the Plasmodium falciparum...

ID or keywords:

Entry

Database: PDB / ID: 6dfk

Title

Crystal structure of the 11S subunit of the Plasmodium falciparum proteasome, PA28

Components

Subunit of proteaseome activator complex,putative

Keywords

PROTEIN BINDING / 11S proteasome subunit / 11S regulatory particle / PA28 / REG / proteasome activator / hydrolase activator

Function / homology

Function and homology information

proteasome activator complex / positive regulation of endopeptidase activity / regulation of G1/S transition of mitotic cell cycle / endopeptidase activator activity / regulation of proteasomal protein catabolic process /

nucleoplasm /

cytoplasm

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Xie, S.C. / Metcalfe, R.D. / Gillett, D.L. / Tilley, L. / Griffin, M.D.W.

Funding support

Australia, 4items

Organization	Grant number	Country
National Health and Medical Research Council (NHMRC, Australia)		Australia
Australian Research Council (ARC)		Australia
Global Health Innovative Technology Fund
GSK Tres Cantos Open Lab Foundation

Validation Report

Summary

Full report

About validation report

History

Deposition	May 15, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2019	Provider: repository / Type: Initial release
Revision 1.1	Aug 14, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 6, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Related structure data

Related structure data	20073C 9257C 9258C 9259C 6muvC 6muwC 6muxC 1avoS S: Starting model for refinement C: citing same article (ref.)
Similar-shape strucutres	Search similar-shape structures by Omokage search (details)

Deposited unit

A: Subunit of proteaseome activator complex,putative

B: Subunit of proteaseome activator complex,putative

C: Subunit of proteaseome activator complex,putative

D: Subunit of proteaseome activator complex,putative

E: Subunit of proteaseome activator complex,putative

F: Subunit of proteaseome activator complex,putative

G: Subunit of proteaseome activator complex,putative

H: Subunit of proteaseome activator complex,putative

I: Subunit of proteaseome activator complex,putative

J: Subunit of proteaseome activator complex,putative

K: Subunit of proteaseome activator complex,putative

L: Subunit of proteaseome activator complex,putative

M: Subunit of proteaseome activator complex,putative

N: Subunit of proteaseome activator complex,putative

hetero molecules

471 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Subunit of proteaseome activator complex,putative

B: Subunit of proteaseome activator complex,putative

C: Subunit of proteaseome activator complex,putative

D: Subunit of proteaseome activator complex,putative

E: Subunit of proteaseome activator complex,putative

F: Subunit of proteaseome activator complex,putative

G: Subunit of proteaseome activator complex,putative

hetero molecules

defined by author&software
Evidence: SAXS
236 kDa, 7 polymers
Download structure data
Search similar-shape structures of this assembly by Omokage search (details)

2

H: Subunit of proteaseome activator complex,putative

I: Subunit of proteaseome activator complex,putative

J: Subunit of proteaseome activator complex,putative

K: Subunit of proteaseome activator complex,putative

L: Subunit of proteaseome activator complex,putative

M: Subunit of proteaseome activator complex,putative

N: Subunit of proteaseome activator complex,putative

hetero molecules

defined by author&software
Evidence: SAXS
236 kDa, 7 polymers
Download structure data
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

γ

α

β

Length a, b, c (Å)	166.485, 166.485, 399.162
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Subunit of proteaseome activator complex,putative Mass: 33235.824 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PF3D7_0907700 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I374
#2: Chemical	... ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: SO₄

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.44 Å³/Da / Density % sol: 64.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20 mM HEPES, 2 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 3.1→48.89 Å / Num. obs: 116975 / % possible obs: 100 % / Redundancy: 10.4 % / B_iso Wilson estimate: 60.6 Å² / CC_1/2: 0.996 / R_pim(I) all: 0.131 / R_rim(I) all: 0.305 / Net I/σ(I): 7.5
Reflection shell	Resolution: 3.1→3.15 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5711 / CC_1/2: 0.513 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1AVO

1avo

Resolution: 3.1→48.89 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 22.42

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2251	3534	3.02 %	Random; Thin shells
R_work	0.1817	-	-	-
Obs	0.183	116839	99.95 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.1→48.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	26198	0	300	0	26498

Refine LS restraints

Refinement-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	26942
X-RAY DIFFRACTION	f_angle_d	0.636	36381
X-RAY DIFFRACTION	f_dihedral_angle_d	1.846	16405
X-RAY DIFFRACTION	f_chiral_restr	0.045	3963
X-RAY DIFFRACTION	f_plane_restr	0.003	4545

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refinement-ID	% reflection obs (%)
3.1-3.2108	0.3174	227	0.299	11348	X-RAY DIFFRACTION	100
3.2108-3.3393	0.3108	534	0.262	11020	X-RAY DIFFRACTION	100
3.3393-3.4912	0.2671	193	0.237	11333	X-RAY DIFFRACTION	100
3.4912-3.6753	0.2869	358	0.2173	11225	X-RAY DIFFRACTION	100
3.6753-3.9054	0.2399	403	0.1859	11185	X-RAY DIFFRACTION	100
3.9054-4.2068	0.1902	449	0.1497	11179	X-RAY DIFFRACTION	100
4.2068-4.6299	0.1811	264	0.1366	11437	X-RAY DIFFRACTION	100
4.6299-5.2991	0.192	362	0.1413	11326	X-RAY DIFFRACTION	100
5.2991-6.6737	0.2213	366	0.1888	11479	X-RAY DIFFRACTION	100
6.6737-48.8963	0.2081	378	0.1695	11773	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refinement-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	0.577	-0.2261	0.1823	1.7646	-0.3382	1.5725	0.1433	-0.1079	-0.1377	0.1671	-0.028	-0.0471	0.3541	-0.0557	-0.0893	0.5749	-0.1187	-0.0335	0.3402	0.0559	0.3769	-69.244	25.2663	16.7894
2	0.8044	-0.6386	0.101	2.9425	0.0779	1.2959	0.0473	-0.0281	-0.0859	-0.088	-0.0197	0.1095	0.1952	-0.1856	-0.0608	0.3818	-0.1402	-0.0353	0.3731	0.0161	0.278	-72.3984	33.4304	-4.7258
3	1.2078	-0.4785	-0.5381	1.7677	0.45	1.4733	-0.0578	-0.019	-0.0345	-0.0694	0.1104	-0.0794	0.0544	0.1669	-0.0831	0.3565	-0.0835	-0.0605	0.4272	0.019	0.2811	-62.4323	51.0072	-15.8381
4	1.8457	-0.2905	-0.7496	1.6304	0.7187	2.4639	-0.1579	0.188	0.1565	0.2171	0.135	-0.0834	-0.0753	0.1253	0.0046	0.4298	-0.1416	-0.0958	0.3853	0.0523	0.4073	-51.8032	68.0786	-5.3335
5	1.9128	0.2708	-0.5844	0.7682	0.0351	1.75	0.0369	-0.2534	-0.0902	0.3293	-0.0484	-0.1825	-0.2534	0.425	-0.0316	0.6232	-0.1695	-0.2063	0.4672	0.0371	0.5482	-41.5932	69.0019	16.1023
6	4.3112	0.788	-0.6363	0.6491	-0.573	1.2731	0.1497	-0.3121	-0.0005	0.4095	-0.1323	-0.1698	-0.1933	0.2365	-0.0355	0.8859	-0.1276	-0.22	0.4688	-0.0067	0.4622	-49.1643	56.3742	34.3795
7	3.2273	-0.2792	0.8874	1.1976	-0.3372	1.0995	0.2332	-0.1299	-0.1093	0.2816	-0.1707	-0.2653	0.0386	0.0687	-0.0896	0.7812	-0.0353	-0.0882	0.4489	0.0886	0.3726	-58.1984	35.3818	34.4325
8	1.0274	-0.4002	-0.0481	1.8796	0.8764	1.237	-0.0257	-0.0543	0.1217	-0.0426	0.0227	-0.0728	-0.1013	0.0544	0.0068	0.38	-0.0865	-0.0159	0.4518	0.0572	0.2797	-77.4121	70.6099	-31.9352
9	1.0289	0.7126	0.2176	2.3516	0.7627	1.4423	0.0294	0.1342	-0.0404	0.0723	0.0358	-0.0214	-0.0171	0.1341	-0.0938	0.2615	-0.0103	0.0061	0.5583	0.0768	0.3087	-64.0755	65.3467	-49.6097
10	1.3131	0.9549	0.2214	1.3975	0.0326	0.9126	-0.0592	0.492	0.0242	-0.11	0.1421	-0.0093	-0.0826	0.2436	-0.0853	0.3344	0.0481	0.0519	0.7291	0.0359	0.3273	-67.8537	67.2277	-72.8265
11	1.6006	0.735	-0.0441	1.1848	-0.4563	1.0399	-0.0388	0.4428	0.1435	-0.0676	0.138	0.1082	-0.0891	0.0333	-0.0893	0.418	0.0804	0.0125	0.7572	0.0085	0.3523	-87.4089	68.2105	-83.1168
12	1.3943	0.5177	-0.3413	1.5255	-0.9645	1.2966	0.0021	0.3119	0.105	-0.0644	0.0636	-0.0453	0.0079	-0.103	-0.0584	0.2825	0.0299	-0.0326	0.6515	-0.0049	0.3971	-108.5677	67.6756	-73.2314
13	1.2784	-0.6707	0.1865	1.7967	-0.2483	0.7343	-0.0595	0.0284	0.1259	0.1554	-0.0024	-0.0042	-0.1622	-0.208	0.0014	0.2814	0.033	0.0075	0.5934	-0.0424	0.3854	-114.6071	73.4597	-51.1607
14	1.4348	-1.0116	0.4963	2.9118	0.0744	1.2705	0.0269	-0.2318	0.0697	0.0902	-0.0292	0.0509	-0.0315	-0.1859	-0.0141	0.3238	-0.0634	0.0399	0.4814	0.0034	0.2592	-100.6106	69.9009	-32.8398

Refinement TLS group

ID	Refinement-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 6 through 269)
2	X-RAY DIFFRACTION	2	(chain 'B' and resid 6 through 270)
3	X-RAY DIFFRACTION	3	(chain 'C' and resid 6 through 270)
4	X-RAY DIFFRACTION	4	(chain 'D' and resid 6 through 269)
5	X-RAY DIFFRACTION	5	(chain 'E' and resid 7 through 270)
6	X-RAY DIFFRACTION	6	(chain 'F' and resid 8 through 269)
7	X-RAY DIFFRACTION	7	(chain 'G' and resid 6 through 269)
8	X-RAY DIFFRACTION	8	(chain 'H' and resid 6 through 269)
9	X-RAY DIFFRACTION	9	(chain 'I' and resid 5 through 270)
10	X-RAY DIFFRACTION	10	(chain 'J' and resid 6 through 270)
11	X-RAY DIFFRACTION	11	(chain 'K' and resid 0 through 270)
12	X-RAY DIFFRACTION	12	(chain 'L' and resid 5 through 269)
13	X-RAY DIFFRACTION	13	(chain 'M' and resid 6 through 270)
14	X-RAY DIFFRACTION	14	(chain 'N' and resid 6 through 269)

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