PDB-3qs1: Crystal structure of KNI-10006 complex of Plasmepsin I (PMI) from...

ID or keywords:

Entry

Database: PDB / ID: 3qs1

Title

Crystal structure of KNI-10006 complex of Plasmepsin I (PMI) from Plasmodium falciparum

Components

Plasmepsin-1

Keywords

HYDROLASE/HYDROLASE INHIBITOR /

Aspartic protease /

Malaria / KNI / HYDROLASE-HYDROLASE INHIBITOR complex

Function / homology

Function and homology information

plasmepsin I /

cytostome / acquisition of nutrients from host / vacuolar lumen /

food vacuole / vacuolar membrane / aspartic-type endopeptidase activity /

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Bhaumik, P. / Gustchina, A. / Wlodawer, A.

Citation

Journal: J.Struct.Biol. / Year: 2011
Title: Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum.
Authors: Bhaumik, P. / Horimoto, Y. / Xiao, H. / Miura, T. / Hidaka, K. / Kiso, Y. / Wlodawer, A. / Yada, R.Y. / Gustchina, A.

History

Deposition	Feb 19, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 11, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Dec 12, 2012	Group: Other

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3qs1.cif.gz	522.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3qs1.ent.gz	453.4 KB	Display	PDB format
PDBx/mmJSON format	3qs1.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/qs/3qs1 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/3qs1	HTTPS FTP

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Related structure data

Related structure data	3qrvC C: citing same article (ref.)
Similar structure data	5w3y-d 4i1m-d 3nw4-1 4nnd-d 5w40-d 2rcy-d 6o8u-d 6iy1-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Plasmepsin-1

B: Plasmepsin-1

C: Plasmepsin-1

D: Plasmepsin-1

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	93.690, 93.690, 160.120
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	Plasmepsin-1 / / Aspartic hemoglobinase I / PfAPG Mass: 37845.676 Da / Num. of mol.: 4 / Fragment: UNP residues 117-452 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PMI / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) pLysS / References: UniProt: P39898, plasmepsin I
#2: Chemical	ChemComp-006 / (4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide / KNI-10006 Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 631.782 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₅H₄₁N₃O₆S / References: KNI-10006
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.32 Å³/Da / Density % sol: 47.01 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25 % PEG 2000 MME, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 20, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.1→40 Å / Num. all: 25066 / Num. obs: 24816 / % possible obs: 99 % / Redundancy: 5.8 % / R_merge(I) obs: 0.144 / Net I/σ(I): 11.8
Reflection shell	Resolution: 3.1→3.2 Å / Redundancy: 5.8 % / R_merge(I) obs: 0.1636 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2227 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
PHASER		phasing
REFMAC	5.5.0104	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.1→30 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.869 / SU B: 67.648 / SU ML: 0.551 / Cross valid method: THROUGHOUT / ESU R Free: 0.635 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.29965	1240	5 %	RANDOM
R_work	0.21104	-	-	-
obs	0.21544	23562	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 49.496 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.01 Å²	0 Å²	0 Å²
2-	-	0.01 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10406	0	240	0	10646

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.022	10928
X-RAY DIFFRACTION	r_angle_refined_deg	2.161	1.975	14852
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.803	5	1302
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.653	25.44	500
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	25.029	15	1752
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.753	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.145	0.2	1634
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	8308
X-RAY DIFFRACTION	r_mcbond_it	0.484	1.5	6514
X-RAY DIFFRACTION	r_mcangle_it	0.969	2	10602
X-RAY DIFFRACTION	r_scbond_it	1.486	3	4414
X-RAY DIFFRACTION	r_scangle_it	2.483	4.5	4250

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.398	89	-
R_work	0.313	1704	-
obs	-	-	100 %

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	2.1841	0.1075	-1.662	1.9864	0.7667	3.8596	0.0175	0.0986	-0.0012	0.0679	-0.0647	0.1178	0.0025	-0.1011	0.0471	0.0856	0.0659	-0.0355	0.1901	0.0037	0.217	28.6247	-0.4521	-3.9065
2	72.4359	54.9519	11.6174	65.2987	35.5384	32.3063	3.4785	1.9974	0.2108	3.8799	0.2989	-2.4819	1.518	-0.5754	-3.7774	0.9238	-0.0658	0.4536	0.4251	-0.2201	1.8901	12.9861	-6.6076	22.9081
3	1.1502	-0.2962	-0.3155	0.2119	0.3263	3.6754	0.3592	-0.2893	-0.0608	0.1818	0.1846	0.0957	0.5316	-0.0804	-0.5439	0.6764	0.0562	0.0865	0.3995	0.0386	0.3973	18.8556	-9.5911	17.366
4	14.398	18.5156	-5.3608	28.3006	-25.0168	76.156	1.8214	-0.3032	-0.0265	2.2268	0.0889	0.6432	-0.9009	-0.3846	-1.9102	1.022	-0.0149	0.1313	1.1517	0.2229	0.8702	10.5242	-17.5625	21.8927
5	1.369	1.8451	-0.2276	2.6337	-0.0196	0.6385	0.18	-0.098	0.099	0.2954	-0.122	0.0857	0.027	0.0045	-0.058	0.213	0.0458	0.0627	0.2693	-0.0077	0.2307	11.9191	-7.2566	11.1571
6	1.7646	-0.01	0.185	1.6391	0.8159	3.809	0.1166	-0.1544	-0.157	0.0191	-0.0846	-0.1226	0.205	0.1422	-0.0319	0.1884	0.078	-0.0304	0.2363	0.0477	0.3657	22.1837	-46.0719	16.5717
7	6.5544	-30.4732	3.6061	142.1752	-21.642	50.1113	0.7835	-0.1211	0.4728	-3.7308	0.899	-1.9684	2.6128	-2.7386	-1.6825	0.3957	-0.0304	0.0371	0.9517	0.1245	0.7718	22.9956	-40.4677	-14.5913
8	2.1677	2.7031	-0.8627	5.0457	-1.2348	0.7019	0.1364	0.1828	0.196	-0.662	0.0739	-0.2128	0.2084	0.4402	-0.2102	0.5205	0.3322	0.0994	0.8047	-0.099	0.4392	25.3853	-37.5186	-6.8406
9	9.6604	-15.0134	4.863	30.8924	-25.6345	45.6863	1.1137	-0.4179	-1.443	-1.8996	0.5745	2.6308	0.8695	0.0163	-1.6883	0.9081	-0.0544	-0.1082	0.657	-0.1379	0.5272	21.021	-29.2153	-15.0593
10	0.7911	-0.7074	0.6804	1.9005	-0.7154	1.3872	0.1167	0.1564	-0.1434	-0.2682	-0.0882	-0.2253	0.2606	0.1257	-0.0285	0.2473	0.1002	0.0887	0.3188	-0.0158	0.265	16.0418	-39.2716	-5.0329
11	3.1652	-0.206	-0.1163	1.7456	-0.0976	2.6401	-0.2026	-0.3689	0.3696	0.236	0.027	-0.1293	-0.26	0.2165	0.1756	0.1863	0.0898	-0.1226	0.3192	-0.017	0.4035	-28.3967	-0.639	-1.0273
12	29.929	-21.81	-5.7919	24.0669	5.3437	1.2852	-0.0081	-3.4757	0.8742	-2.2186	0.2816	-0.7082	-0.2533	0.2926	-0.2735	1.0923	0.0672	0.1661	1.6346	0.0682	0.7402	-13.2653	-10.8032	-26.859
13	5.4837	4.2851	0.6371	5.0913	0.2175	0.1209	0.1763	0.7061	-0.0665	-0.7749	-0.1728	-0.188	0.1778	0.1796	-0.0035	0.5412	0.3018	-0.0284	0.5846	0.1776	0.3671	-18.939	-13.0718	-20.7369
14	56.3873	-18.7361	-8.5237	41.7069	43.5412	48.0029	0.8308	1.6899	4.8691	-0.3779	0.929	-2.5643	-0.1639	1.4049	-1.7598	1.0218	-0.1216	0.3185	0.7638	0.3998	0.7279	-10.574	-21.9638	-24.1705
15	3.817	-2.6383	1.2071	1.9677	-0.7215	1.1014	0.067	0.3242	0.3171	-0.1394	-0.1339	-0.0631	0.1559	0.2405	0.0669	0.283	0.025	0.0096	0.4564	0.1336	0.3801	-11.8789	-9.7673	-15.0489
16	1.764	0.5302	0.6863	1.5264	0.8136	2.6809	-0.089	0.1581	0.0111	-0.3229	0.0584	-0.0783	-0.1361	-0.0584	0.0307	0.5921	-0.1076	-0.0821	0.5218	-0.0848	0.5748	-23.8334	-48.0281	-12.7906
17	72.5153	-20.4348	74.4927	48.9168	9.7233	98.3931	4.534	2.2929	-2.4324	2.029	-1.5909	-0.2121	6.7438	1.5219	-2.9431	1.3787	0.0017	-0.253	1.1083	0.1699	0.6619	-21.637	-35.1867	17.6911
18	2.6859	1.7799	-1.5527	5.3503	1.2373	4.0562	0.3094	0.0142	0.2099	0.5166	-0.0845	0.9039	0.0432	-0.9912	-0.2249	0.3297	0.0026	-0.0361	0.6703	0.0245	0.5188	-25.5957	-35.453	8.0521
19	120.696	2.1796	44.3415	31.9965	42.6442	71.1314	4.2594	-1.4829	-2.4212	1.2007	-1.4475	-1.6013	2.7343	-2.7842	-2.8119	1.4546	0.3076	0.1544	0.8203	0.2928	0.3101	-20.2867	-25.7754	15.3461
20	2.4466	1.8915	1.2678	2.9899	1.3688	1.427	0.1549	0.1081	-0.3402	-0.0166	-0.0179	0.1111	0.3114	-0.4407	-0.137	0.334	-0.0234	-0.0649	0.4471	0.0174	0.3345	-16.3008	-37.8098	6.8405

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 194
2	X-RAY DIFFRACTION	2	A	195 - 201
3	X-RAY DIFFRACTION	3	A	203 - 229
4	X-RAY DIFFRACTION	4	A	230 - 234
5	X-RAY DIFFRACTION	5	A	235 - 328
6	X-RAY DIFFRACTION	6	B	0 - 194
7	X-RAY DIFFRACTION	7	B	195 - 201
8	X-RAY DIFFRACTION	8	B	203 - 229
9	X-RAY DIFFRACTION	9	B	230 - 234
10	X-RAY DIFFRACTION	10	B	235 - 328
11	X-RAY DIFFRACTION	11	C	1 - 194
12	X-RAY DIFFRACTION	12	C	195 - 201
13	X-RAY DIFFRACTION	13	C	203 - 229
14	X-RAY DIFFRACTION	14	C	230 - 234
15	X-RAY DIFFRACTION	15	C	235 - 328
16	X-RAY DIFFRACTION	16	D	1 - 194
17	X-RAY DIFFRACTION	17	D	195 - 201
18	X-RAY DIFFRACTION	18	D	203 - 229
19	X-RAY DIFFRACTION	19	D	230 - 234
20	X-RAY DIFFRACTION	20	D	235 - 328

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