PDB-4m1n: Crystal structure of Plasmodium falciparum ubiquitin conjugating ...

ID or keywords:

Entry

Database: PDB / ID: 4m1n

Title

Crystal structure of Plasmodium falciparum ubiquitin conjugating enzyme UBC9

Components

Ubiquitin conjugating enzyme UBC9

Keywords

LIGASE /

SUMO /

E2 enzyme

Function / homology

Function and homology information

SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of SUMOylation proteins / SUMOylation of chromatin organization proteins / SUMOylation of RNA binding proteins / SUMOylation of DNA replication proteins / SUMO conjugating enzyme activity / protein sumoylation /

ligase activity /

ATP binding /

nucleus
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Boucher, L.E. / Reiter, K.H. / Bosch, J. / Matunis, J.M.

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Identification of Biochemically Distinct Properties of the Small Ubiquitin-related Modifier (SUMO) Conjugation Pathway in Plasmodium falciparum.
Authors: Reiter, K. / Mukhopadhyay, D. / Zhang, H. / Boucher, L.E. / Kumar, N. / Bosch, J. / Matunis, M.J.

History

Deposition	Aug 3, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 21, 2013	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3	Sep 20, 2023	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4m1n.cif.gz	226.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4m1n.ent.gz	183.2 KB	Display	PDB format
PDBx/mmJSON format	4m1n.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/m1/4m1n ftp://data.pdbj.org/pub/pdb/validation_reports/m1/4m1n	HTTPS FTP

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Related structure data

Related structure data	4jueSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4jue-4 4l83-d 6tqs-1 6gv3-d 1a3s-d 6fpc-4 6nyd-d 4jue-2 6ndt-d 6dxn-3 Search similar-shape structures by Omokage search (details) 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

Related structure data

4jueSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (6) #60 - Dec 2004 Ubiquitin similarity (6)

Deposited unit

A: Ubiquitin conjugating enzyme UBC9

B: Ubiquitin conjugating enzyme UBC9

C: Ubiquitin conjugating enzyme UBC9

hetero molecules

54.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ubiquitin conjugating enzyme UBC9

hetero molecules

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

2

B: Ubiquitin conjugating enzyme UBC9

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

3

C: Ubiquitin conjugating enzyme UBC9

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

Unit cell

Length a, b, c (Å)	85.190, 90.770, 122.740
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-370- HOH
2	1	A-492- HOH
3	1	A-579- HOH
4	1	B-240- HOH
5	1	B-251- HOH
6	1	C-291- HOH
7	1	C-292- HOH

#1: Protein	Ubiquitin conjugating enzyme UBC9 Mass: 18286.998 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: PF3D7_0915100, PFI0740c / Plasmid: WTPfUbc9-pGex4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: Q8I301
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 956 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.16 Å³/Da / Density % sol: 43.12 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M NaF, 20% PEG3350 Cryo: 30% PEG3350, 10% glycerol, 0.2M NaF, 100mM glycine, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL7-1 / Wavelength: 1.1271 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2013

Radiation

Monochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1271 Å / Relative weight: 1

Reflection

Resolution: 1.5→31 Å / Num. all: 76146 / Num. obs: 76146 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.16 % / R_merge(I) obs: 0.126 / Net I/σ(I): 8.6

Reflection shell

Resolution (Å)	Diffraction-ID	% possible all
1.5-1.54	1	99
1.55-2.11	1	100
2.12-6.7	1	100
6.71-31	1	95.6

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Processing

Software

Name	Version	Classification
Blu-Ice	ice	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 4JUE

4jue

Resolution: 1.5→31.059 Å / SU ML: 0.14 / σ(F): 1.36 / Phase error: 18.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1958	3805	5 %
R_work	0.1635	-	-
obs	0.1651	76123	99.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→31.059 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3837	0	1	956	4794

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4045
X-RAY DIFFRACTION	f_angle_d	1.195	5491
X-RAY DIFFRACTION	f_dihedral_angle_d	11.559	1604
X-RAY DIFFRACTION	f_chiral_restr	0.049	563
X-RAY DIFFRACTION	f_plane_restr	0.007	718

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 (%)
1.5-1.519	0.3255	142	0.2767	2687	X-RAY DIFFRACTION	100
1.519-1.539	0.2632	137	0.2491	2614	X-RAY DIFFRACTION	100
1.539-1.5601	0.2453	141	0.2224	2682	X-RAY DIFFRACTION	100
1.5601-1.5823	0.2521	139	0.202	2639	X-RAY DIFFRACTION	100
1.5823-1.606	0.1972	140	0.1876	2653	X-RAY DIFFRACTION	100
1.606-1.6311	0.2411	139	0.1907	2650	X-RAY DIFFRACTION	100
1.6311-1.6578	0.2338	140	0.1749	2657	X-RAY DIFFRACTION	100
1.6578-1.6864	0.2137	140	0.1835	2648	X-RAY DIFFRACTION	100
1.6864-1.717	0.2079	140	0.1702	2664	X-RAY DIFFRACTION	100
1.717-1.7501	0.239	139	0.173	2650	X-RAY DIFFRACTION	100
1.7501-1.7858	0.1968	142	0.1638	2688	X-RAY DIFFRACTION	100
1.7858-1.8246	0.1992	140	0.1736	2658	X-RAY DIFFRACTION	100
1.8246-1.8671	0.2091	139	0.1703	2638	X-RAY DIFFRACTION	100
1.8671-1.9137	0.2112	140	0.1726	2669	X-RAY DIFFRACTION	100
1.9137-1.9655	0.2004	142	0.1562	2692	X-RAY DIFFRACTION	100
1.9655-2.0233	0.1971	140	0.1576	2665	X-RAY DIFFRACTION	100
2.0233-2.0886	0.1825	140	0.1495	2669	X-RAY DIFFRACTION	100
2.0886-2.1632	0.1568	141	0.1504	2672	X-RAY DIFFRACTION	100
2.1632-2.2498	0.1716	140	0.1505	2666	X-RAY DIFFRACTION	100
2.2498-2.3522	0.216	141	0.1618	2676	X-RAY DIFFRACTION	100
2.3522-2.4761	0.1982	142	0.1594	2699	X-RAY DIFFRACTION	100
2.4761-2.6312	0.1943	142	0.167	2683	X-RAY DIFFRACTION	100
2.6312-2.8342	0.195	143	0.1578	2722	X-RAY DIFFRACTION	100
2.8342-3.1192	0.1959	143	0.1643	2711	X-RAY DIFFRACTION	100
3.1192-3.57	0.1985	142	0.1489	2709	X-RAY DIFFRACTION	100
3.57-4.4956	0.1615	145	0.1352	2749	X-RAY DIFFRACTION	100
4.4956-31.0654	0.1723	146	0.1691	2808	X-RAY DIFFRACTION	98

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	1.3192	0.8764	0.3334	2.1152	0.228	1.1839	0.0188	0.026	0.0517	0.2547	-0.126	-0.3294	-0.4137	0.4602	-0.095	0.1829	-0.2574	-0.0341	0.1815	0.0983	0.208	-0.5197	-17.2316	16.1789
2	1.6642	1.2876	0.5469	3.5187	0.651	2.28	0.1188	0.0516	0.35	0.0255	-0.2138	0.1049	-0.5448	-0.0995	0.0458	0.1991	-0.0053	0.0259	0.0856	0.0255	0.1213	-10.7643	-18.4267	11.916
3	1.4911	0.7091	0.4379	4.6617	1.3997	2.5106	0.0429	0.1118	-0.0082	-0.306	0.0078	-0.2151	-0.1415	0.1145	-0.059	0.0532	-0.0027	0.0225	0.0695	0.0113	0.0566	-13.642	-33.2454	9.0348
4	3.7694	-0.4206	2.4508	2.8437	1.5927	2.8403	-0.0196	-0.3748	0.1679	0.8054	-0.0785	-0.168	-0.5234	0.1528	0.0559	0.2666	-0.0746	-0.0196	0.1516	0.0062	0.0978	-7.0741	-20.2932	26.7482
5	1.4721	0.4448	-0.1768	2.12	0.1752	0.93	0.0614	-0.048	0.0225	0.0805	-0.0935	0.0446	0.0288	0.0128	0.0304	0.0225	0.0052	-0.005	0.0795	0.0038	0.0713	-17.5092	-32.6832	19.5066
6	1.413	0.8808	-0.2217	1.5994	0.6679	1.4857	0.0153	-0.0819	-0.0109	0.2278	-0.0577	-0.2452	-0.0035	0.539	-0.0559	0.0367	-0.0044	-0.0317	0.1541	0.0277	0.1184	-5.455	-31.8844	20.7565
7	5.7496	-1.4711	-2.7481	2.0262	0.8163	4.3193	-0.1201	-0.5441	-0.4021	0.3345	0.0558	-0.1308	0.5309	0.3655	0.0507	0.1499	0.0227	-0.0207	0.1202	0.0408	0.1481	-15.346	-42.7321	21.7595
8	0.3785	-1.0483	-1.8068	3.4738	5.7646	9.6429	0.0343	-0.0076	0.0261	0.132	-0.0734	0.1513	0.2779	-0.1124	0.061	0.0722	-0.0315	-0.005	0.0909	0.0143	0.1283	-23.8615	-47.4513	18.3358
9	1.8235	1.7389	-1.1673	7.6168	-3.9618	4.2108	0.0434	0.1334	0.0082	-0.1993	0.0613	0.3186	-0.0605	-0.1918	-0.0868	0.0768	0.0046	-0.0241	0.0845	-0.0135	0.0628	-21.8094	-40.3151	5.2726
10	2.8934	-0.0575	-0.4754	2.4656	0.4332	4.2913	0.0861	-0.0158	0.1248	-0.0247	0.1783	-0.5029	-0.3088	0.6957	-0.1196	0.0855	-0.0586	0.0051	0.1427	-0.0165	0.1638	-28.9325	-16.3502	18.9448
11	0.657	0.5216	0.3713	1.0486	0.6617	1.7289	0.0271	-0.0158	0.0461	-0.0122	-0.0096	0.0531	-0.0231	0.0655	-0.0273	0.0237	0.0067	-0.0014	0.0769	-0.0064	0.0891	-39.7074	-26.8264	17.7849
12	2.2965	1.8669	-0.0612	2.4637	0.2324	1.0934	0.0237	-0.0702	-0.2381	0.147	-0.0057	-0.1989	0.3132	0.0731	-0.0004	0.1106	0.0239	-0.0282	0.0857	0.0126	0.096	-41.498	-41.0503	16.0243
13	1.5733	0.5302	-0.3995	2.9155	-3.5359	4.343	-0.0225	0.1099	-0.0401	-0.0549	-0.0334	-0.0241	0.0559	-0.1162	0.0186	0.0831	0.0044	-0.0123	0.0813	-0.0154	0.0655	-48.9505	-38.3508	3.8985
14	3.0544	-0.1217	-0.4689	3.2664	-1.5452	5.4993	-0.0127	0.0621	0.1342	0.0232	0.0427	0.2587	-0.272	-0.3426	-0.1039	0.0523	0.0113	-0.0176	0.0637	-0.0214	0.0933	-25.4132	-13.6805	43.8019
15	1.1792	-0.7722	-0.2921	3.3843	-1.2667	2.0634	-0.0168	-0.2008	0.064	0.3062	-0.0808	-0.1342	0.029	0.2521	0.0468	0.1143	0.0157	-0.0041	0.1165	-0.0113	0.0612	-16.5802	-23.3018	51.4571
16	1.3786	-1.0185	1.0172	2.525	-1.3851	1.5384	-0.038	0.0748	-0.0167	0.0357	-0.0586	-0.0959	0.2188	0.2064	0.129	0.0966	0.0325	0.0263	0.1003	0.0019	0.0723	-14.68	-25.4837	42.1471
17	0.9247	-0.8758	-0.2948	1.1226	-0.1563	0.959	-0.1151	0.0781	-0.0961	-0.1567	0.0512	0.0192	0.7547	-0.0559	0.0821	0.2502	0.0353	0.0339	0.0685	-0.0221	0.0797	-19.4044	-33.8625	40.0295
18	1.11	-0.2885	0.0623	1.745	-1.0008	2.1002	0.0904	0.0559	-0.0754	-0.0548	0.083	-0.0566	-0.127	-0.0528	-0.1446	0.3639	0.1456	0.087	0.1043	0.0182	0.2062	-9.4477	-49.5557	42.2686
19	1.309	0.6124	0.0498	7.043	4.0127	2.4723	-0.0063	-0.2974	-0.1037	0.3216	-0.1952	-0.1747	0.3773	0.1284	0.1219	0.3188	0.1063	0.0175	0.2236	0.0632	0.1414	-9.7242	-41.7171	56.1067

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 46 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 63 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 64 through 73 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 74 through 97 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 98 through 121 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 122 through 130 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 131 through 140 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 141 through 159 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1 through 17 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 18 through 108 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 109 through 140 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 141 through 159 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 0 through 17 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 18 through 56 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 57 through 82 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 83 through 130 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 131 through 140 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 141 through 159 )

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Yorodumi