PDB-2we6: Crystal Structure of Plasmodium falciparum Ubiquitin Carboxyl- te...

ID or keywords:

Entry

Database: PDB / ID: 2we6

Title

Crystal Structure of Plasmodium falciparum Ubiquitin Carboxyl- terminal Hydrolase 3 (UCHL3)

Components

UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3

Keywords

HYDROLASE / CYSTEIN PROTEINASE / DENEDDYLATING ENZYME / UBIQUITIN ISOPEPTIDASE / DEUBIQUITINATING ENZYME / PEPTIDASE_C12 / UCH-L SUPERFAMILY

Function / homology

Function and homology information

Synthesis of active ubiquitin: roles of E1 and E2 enzymes / UCH proteinases / Neddylation / deNEDDylase activity / protein deneddylation / protein deubiquitination / ubiquitin ligase complex / ubiquitin binding / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 ...
Similarity search - Function

Biological species

PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.42 Å

Authors

Weihofen, W.A. / Artavanis-Tsakonas, K. / Gaudet, R. / Ploegh, H.L.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Characterization and Structural Studies of the Plasmodium Falciparum Ubiquitin and Nedd8 Hydrolase Uchl3.
Authors: Artavanis-Tsakonas, K. / Weihofen, W.A. / Antos, J.M. / Coleman, B.I. / Comeaux, C.A. / Duraisingh, M.T. / Gaudet, R. / Ploegh, H.L.

History

Deposition	Mar 27, 2009	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 29, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2we6.cif.gz	99.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2we6.ent.gz	77.7 KB	Display	PDB format
PDBx/mmJSON format	2we6.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/we/2we6 ftp://data.pdbj.org/pub/pdb/validation_reports/we/2we6	HTTPS FTP

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Related structure data

Related structure data	2wdtSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2voa-2 5inm-4 5cml-1 3fzi-d 6lpm-d 6cac-3 5inn-1 5vac-d 2jc4-d 6cac-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3

B: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3

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

1

A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3

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

2

B: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3

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

Unit cell

Length a, b, c (Å)	168.343, 44.979, 99.534
Angle α, β, γ (deg.)	90.00, 121.79, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3 / UCHL3 / UCH-L3 / UBIQUITIN THIOLESTERASE Mass: 26930.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum) Strain: CLONE 3D7 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IKM8*PLUS, ubiquitinyl hydrolase 1
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	CDNA OF PLASMODIUM FALCIPARUM UCHL3 WAS GENERATED AS DESCRIBED IN FRICKEL ET AL., CELL. MICROBIOL. ...CDNA OF PLASMODIUM FALCIPARUM UCHL3 WAS GENERATED AS DESCRIBED IN FRICKEL ET AL., CELL. MICROBIOL. 2007, 9, 1601-10. SEQUENCE DIFFERS FROM THE UCHL3 SEQUENCE ANNOTATED IN THE PLASMODIUM DATABASE (PLASMODB ENTRY PF14- 0576).

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.2 Å³/Da / Density % sol: 62 % / Description: NONE
Crystal grow	pH: 9 Details: 100 MM BICINE PH 9.0, 300 MM MGCL2, 25% PEG 2000, 15% GLYCEROL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5417
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 20, 2007 / Details: OSMIC MIRRORS
Radiation	Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5417 Å / Relative weight: 1
Reflection	Resolution: 2.42→30 Å / Num. obs: 24494 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / R_merge(I) obs: 0.08 / Net I/σ(I): 11.1
Reflection shell	Resolution: 2.42→2.46 Å / Redundancy: 2.7 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 2.3 / % possible all: 96.2

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Processing

Software

Name	Version	Classification
REFMAC	5.4.0066	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WDT

2wdt

Resolution: 2.42→28.21 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.909 / SU B: 15.849 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-4, 59-74 AND 229-232 OF CHAIN A ARE DISORDERED. RESIDUES 1-3, 59-75 AND 228-232 OF CHAIN B ARE DISORDERED.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.251	1024	4.2 %	RANDOM
R_work	0.218	-	-	-
obs	0.219	23466	99 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 35.98 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.32 Å²	0 Å²	0.25 Å²
2-	-	0 Å²	0 Å²
3-	-	-	-0.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.42→28.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3394	0	0	123	3517

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	3470
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2332
X-RAY DIFFRACTION	r_angle_refined_deg	1.28	1.95	4693
X-RAY DIFFRACTION	r_angle_other_deg	0.872	3	5712
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.028	5	411
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.214	25.767	189
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.7	15	611
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.989	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	509
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	3853
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	685
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.404	1.5	2067
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.744	2	3357
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.181	3	1403
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.84	4.5	1336
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.42→2.48 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.359	72	-
R_work	0.302	1642	-
obs	-	-	94.59 %

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	13.8147	0.447	-4.7078	2.3043	4.2271	9.9802	-0.0563	-1.3387	-0.0119	0.5873	-0.2631	-0.4748	0.983	0.8334	0.3194	0.0143	0.0435	-0.166	0.1857	0.0132	-0.056	12.202	-22.774	-32.988
2	1.3097	-2.4026	-2.5697	13.9612	-1.5102	9.0969	-0.175	-0.1473	0.2065	-0.0291	-0.1228	-0.9812	-1.1509	0.676	0.2977	-0.1533	-0.0363	-0.0443	0.0154	-0.0516	-0.0432	10.836	-16.356	-47.383
3	4.3354	-0.5122	0.0462	7.1664	0.8891	2.3346	0.0393	-0.0982	0.6146	-0.02	0.0726	0.0621	-0.2583	0.075	-0.1119	-0.132	0.008	-0.0914	-0.1286	0.0268	-0.0836	-0.162	-11.176	-46.794
4	6.4521	-1.7429	-1.6039	3.1535	-1.2844	4.3176	-0.0759	-0.4142	-0.4812	0.201	0.2048	0.2319	0.1839	0.019	-0.129	-0.1326	0.0457	-0.069	-0.2533	0	-0.1018	-2.63	-19.856	-38.367
5	6.0132	-0.5514	-3.3475	0.818	-1.9166	9.851	0.0277	-0.2597	-0.7902	-0.112	0.0955	0.5982	0.5671	-0.4401	-0.1232	-0.0834	0.0189	-0.058	-0.2147	0.0784	0.1249	-6.503	-29.914	-40.987
6	12.6637	-6.5365	-2.4355	3.8809	4.1384	16.8407	-0.2526	-0.7417	0.1458	0.4437	0.674	0.191	0.5368	-0.0303	-0.4214	0.0105	-0.0095	-0.0079	-0.0873	0.1359	0.0461	-3.609	-26.719	-29.544
7	15.1249	0.514	-2.9624	2.2616	1.0659	3.7972	-0.2218	-0.7861	-1.2911	0.2679	-0.0715	-0.1285	0.6272	0.76	0.2933	-0.0424	0.0928	-0.0699	-0.0433	0.0706	-0.0086	7.665	-29.644	-37.397
8	9.883	1.7951	11.1141	5.8258	-0.1807	13.3782	-0.6926	-0.4541	0.05	0.305	-0.1867	-0.3784	-1.1709	0.1394	0.8793	-0.0434	0.105	-0.0738	0.2575	0.1343	0.0885	19.804	-18.57	-35.636
9	1.7891	-1.5504	-1.9183	8.1538	-2.5674	4.6839	-0.18	-0.2778	0.5089	0.2129	0.0682	-0.0007	-0.1327	0.0589	0.1118	-0.0894	0.0525	-0.0767	-0.2258	-0.0317	-0.0614	-4.086	-10.414	-38.508
10	5.4216	-2.6687	0.2145	6.5701	-0.861	5.8113	-0.1344	-0.4682	0.663	0.6443	0.2726	-0.0905	-0.8842	-0.2603	-0.1382	-0.0848	0.0327	-0.0753	-0.2031	-0.0217	0.0902	-6.662	-4.365	-39.754
11	5.7351	-3.6855	-4.2665	12.3185	-0.4875	4.2219	0.5041	-0.3586	1.3253	1.0648	-0.1546	-1.9182	-0.5714	1.9197	-0.3495	0.5025	-0.0507	-0.2002	0.4777	-0.1994	0.5922	6.193	2.355	-34.741
12	6.875	2.9643	1.0367	17.1851	5.8938	10.2306	0.1951	0.1964	0.458	0.6831	0.217	-0.912	-0.174	0.9451	-0.4121	-0.1123	0.0458	-0.0043	-0.1315	0.1	-0.0198	4.522	-8.577	-46.933
13	12.5079	-2.1405	3.4235	0.9641	2.1055	13.0546	0.2724	-0.1026	0.6044	0.5302	-0.2732	-0.4159	-0.7587	1.4195	0.0008	-0.0583	0.0387	-0.0776	0.0854	-0.029	-0.0534	27.767	-22.045	-60.702
14	14.4996	-3.9632	-2.5581	10.3596	3.6163	1.3686	0.0372	-0.4603	-1.1025	0.6196	-0.154	-0.0448	0.8338	0.1409	0.1168	0.0382	0.0381	-0.0558	0.0106	0	-0.1658	13.39	-28.095	-57.471
15	2.364	0.5296	0.9112	8.6141	2.4839	5.1336	0.071	-0.2084	-0.2409	0.0702	0.0391	0.2522	0.6966	-0.0036	-0.1101	-0.0644	-0.0371	-0.1338	-0.1496	0.0137	-0.1209	10.243	-33.296	-67.568
16	6.3634	1.3787	-0.5291	4.1681	1.9181	6.4493	-0.1424	0.2833	0.3686	-0.2764	0.0947	0.0018	-0.111	0.1821	0.0476	-0.0749	-0.0192	-0.1158	-0.2742	-0.0091	-0.1861	18.019	-24.94	-73.116
17	7.1912	0.8062	-5.512	2.7912	3.3867	10.1629	-0.0722	0.5217	0.8357	-0.5692	0.0458	0.3194	-0.7887	-0.0735	0.0264	0.0954	-0.0512	-0.16	-0.2106	0.0518	-0.054	14.423	-14.784	-76.128
18	13.1041	-4.1594	-5.6836	7.2211	5.7389	12.0058	0.2545	0.2838	0.5185	-0.3239	0.1569	-0.3189	-0.1987	0.6493	-0.4114	0.018	-0.0917	-0.0317	-0.0186	0.0531	-0.0625	26.29	-18.283	-76.875
19	0.2374	0.3955	1.3755	6.2727	-3.3803	13.7027	0.0263	-0.6383	0.3717	-0.3243	-0.0926	-0.2743	-1.1084	0.9628	0.0663	-0.0517	-0.0802	-0.1092	-0.0302	-0.0436	-0.0505	22.251	-15.152	-63.626
20	12.4983	-2.6448	3.6487	6.2206	-3.1214	2.0402	-0.0008	-0.1578	-1.3446	0.4647	0.016	-0.6263	0.161	0.2033	-0.0152	0.067	-0.1411	-0.154	0.2977	-0.0309	0.0221	27.387	-26.365	-52.222
21	8.4757	4.8502	2.1707	7.9035	6.1052	6.0953	0.3566	0.1702	-0.1446	-0.0419	-0.0821	-0.1734	0.7298	0.2398	-0.2745	-0.0293	0.0004	-0.0766	-0.2644	-0.0073	-0.1049	17.381	-34.228	-74.427
22	4.9762	1.8437	0.6338	6.5894	0.824	4.011	0.4633	0.4633	-1.0318	-0.183	0.0298	-0.4128	0.7558	0.4141	-0.4932	0.16	0.0139	-0.189	-0.1732	-0.0667	-0.0383	15.333	-40.406	-76.415
23	12.8984	-4.1703	-0.4729	7.2266	3.3963	12.7484	-0.0811	-1.1238	-0.533	0.6102	-0.4654	-0.8171	1.6544	1.1466	0.5465	0.5327	0.1012	-0.0977	0.267	-0.0148	0.4969	24.031	-47.35	-66.668
24	15.7238	-5.705	0.9243	9.1088	-1.2616	5.1165	-0.1375	-0.9642	-0.7707	0.1678	0.3919	-0.2187	0.3756	0.0764	-0.2544	-0.006	-0.096	-0.0295	-0.0692	-0.02	-0.0383	11.99	-36.196	-63.883

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 9
2	X-RAY DIFFRACTION	2	A	10 - 16
3	X-RAY DIFFRACTION	3	A	17 - 80
4	X-RAY DIFFRACTION	4	A	81 - 108
5	X-RAY DIFFRACTION	5	A	109 - 128
6	X-RAY DIFFRACTION	6	A	129 - 135
7	X-RAY DIFFRACTION	7	A	136 - 147
8	X-RAY DIFFRACTION	8	A	148 - 161
9	X-RAY DIFFRACTION	9	A	162 - 180
10	X-RAY DIFFRACTION	10	A	181 - 206
11	X-RAY DIFFRACTION	11	A	207 - 216
12	X-RAY DIFFRACTION	12	A	217 - 226
13	X-RAY DIFFRACTION	13	B	5 - 9
14	X-RAY DIFFRACTION	14	B	10 - 16
15	X-RAY DIFFRACTION	15	B	17 - 80
16	X-RAY DIFFRACTION	16	B	81 - 108
17	X-RAY DIFFRACTION	17	B	109 - 128
18	X-RAY DIFFRACTION	18	B	129 - 135
19	X-RAY DIFFRACTION	19	B	136 - 147
20	X-RAY DIFFRACTION	20	B	148 - 161
21	X-RAY DIFFRACTION	21	B	162 - 180
22	X-RAY DIFFRACTION	22	B	181 - 206
23	X-RAY DIFFRACTION	23	B	207 - 216
24	X-RAY DIFFRACTION	24	B	217 - 226

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