PDB-4yet: X-ray crystal structure of superoxide dismutase from Babesia bovi...

ID or keywords:

Entry

Database: PDB / ID: 4yet

Title

X-ray crystal structure of superoxide dismutase from Babesia bovis solved by Sulfur SAD

Components

Superoxide dismutase

Keywords

OXIDOREDUCTASE /

superoxide dismutase / SSGCID /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

superoxide dismutase /

superoxide dismutase activity /

metal ion binding
Similarity search - Function

Biological species

Babesia bovis (eukaryote)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 1.75 Å

Authors

Fairman, J.W. / Clifton, M.C. / Abendroth, J. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Iron superoxide dismutases in eukaryotic pathogens: new insights from Apicomplexa and Trypanosoma structures.
Authors: Phan, I.Q. / Davies, D.R. / Moretti, N.S. / Shanmugam, D. / Cestari, I. / Anupama, A. / Fairman, J.W. / Edwards, T.E. / Stuart, K. / Schenkman, S. / Myler, P.J.

History

Deposition	Feb 24, 2015	Deposition site: RCSB / Processing site: RCSB
Supersession	Apr 15, 2015	ID: 4K2W
Revision 1.0	Apr 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 3, 2015	Group: Database references
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_related / pdbx_struct_oper_list Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_related.content_type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.4	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4yet.cif.gz	180.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4yet.ent.gz	143 KB	Display	PDB format
PDBx/mmJSON format	4yet.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ye/4yet ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4yet	HTTPS FTP

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Related structure data

Related structure data	4f2nC 4h3eC C: citing same article (ref.)
Similar structure data	2w7w-d 3esf-2 3h1s-d 4l2b-d 1uer-1 1uer-2 4l2c-1 2bkb-1 3lio-d 4l2d-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: SSGCID-BaboA.01199.a

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#94 - Oct 2007 Superoxide Dismutase similarity (11)

Deposited unit

A: Superoxide dismutase

B: Superoxide dismutase

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	55.750, 69.090, 114.810
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Superoxide dismutase / Mass: 22901.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Babesia bovis (eukaryote) / Gene: Fe-SOD, BBOV_IV011480 / Production host: Escherichia coli (E. coli) / References: UniProt: O15904, superoxide dismutase
#2: Chemical	ChemComp-FE / FE (III) ION / Iron Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.44 Å³/Da / Density % sol: 49.51 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS HCl Ph 8.5, 25% PEG 3350, / PH range: 8.5

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 7, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.54 Å / Relative weight: 1

Reflection

Resolution: 1.75→50 Å / Num. obs: 44891 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / B_iso Wilson estimate: 16.73 Å² / R_merge F obs: 0.059 / R_merge(I) obs: 0.04 / R_rim(I) all: 0.042 / Χ²: 0.973 / Net I/σ(I): 35.95 / Num. measured all: 421159

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.75-1.8	0.375	0.36	4.54	16271	3333	3080	0.399	92.4
1.8-1.84	0.293	0.299	5.77	18154	3211	3053	0.327	95.1
1.84-1.9	0.24	0.24	7.13	18437	3136	3016	0.262	96.2
1.9-1.96	0.166	0.191	8.94	18933	3075	3006	0.208	97.8
1.96-2.02	0.123	0.152	11.26	19094	2980	2938	0.165	98.6
2.02-2.09	0.097	0.127	14.04	19228	2879	2874	0.137	99.8
2.09-2.17	0.069	0.1	19.59	20838	2773	2773	0.107	100
2.17-2.26	0.052	0.083	26.62	23862	2672	2671	0.088	100
2.26-2.36	0.051	0.075	29.68	24676	2589	2588	0.079	100
2.36-2.47	0.04	0.063	34.78	24753	2470	2469	0.067	100
2.47-2.61	0.034	0.058	38.57	25073	2336	2333	0.061	99.9
2.61-2.77	0.031	0.051	42.5	26409	2245	2237	0.053	99.6
2.77-2.96	0.02	0.042	56.62	29317	2104	2103	0.044	100
2.96-3.2	0.017	0.034	64.85	28044	1952	1951	0.036	99.9
3.2-3.5	0.013	0.028	78.9	26094	1813	1812	0.029	99.9
3.5-3.91	0.01	0.025	95.53	23449	1655	1655	0.026	100
3.91-4.52	0.009	0.022	104.38	20324	1467	1464	0.023	99.8
4.52-5.53	0.009	0.021	104.4	17719	1275	1274	0.022	99.9
5.53-7.83	0.011	0.025	91.68	13388	999	999	0.026	100

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.75→44.153 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0.41 / Phase error: 15.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1763	2258	5.05 %	RANDOM
R_work	0.1429	80937	-	-
obs	0.1446	44841	98.64 %	-

Solvent computation

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

Displacement parameters

B_iso max: 53.7 Å² / B_iso mean: 18.488 Å² / B_iso min: 7.52 Å²

Refinement step

Cycle: final / Resolution: 1.75→44.153 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3151	0	2	408	3561
B_iso mean	-	-	10.27	29.87	-
Num. residues	-	-	-	-	398

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3343
X-RAY DIFFRACTION	f_angle_d	1.084	4589
X-RAY DIFFRACTION	f_chiral_restr	0.052	474
X-RAY DIFFRACTION	f_plane_restr	0.006	595
X-RAY DIFFRACTION	f_dihedral_angle_d	12.074	1171

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.75-1.7699	0.2449	166	0.2004	2528	2694	93
1.7699-1.7907	0.2256	124	0.1849	2532	2656	93
1.7907-1.8126	0.214	144	0.1758	2596	2740	95
1.8126-1.8355	0.1963	149	0.1678	2576	2725	95
1.8355-1.8597	0.1962	124	0.1656	2668	2792	95
1.8597-1.8851	0.1835	144	0.1665	2657	2801	97
1.8851-1.9121	0.2128	156	0.1645	2584	2740	96
1.9121-1.9406	0.2397	141	0.1589	2667	2808	98
1.9406-1.9709	0.1815	112	0.1512	2786	2898	99
1.9709-2.0032	0.1934	158	0.1475	2654	2812	98
2.0032-2.0378	0.1998	150	0.1486	2682	2832	100
2.0378-2.0748	0.1842	163	0.1473	2746	2909	100
2.0748-2.1147	0.2123	138	0.1452	2744	2882	100
2.1147-2.1579	0.1734	150	0.1451	2768	2918	100
2.1579-2.2048	0.1842	150	0.1357	2691	2841	100
2.2048-2.2561	0.1818	146	0.1372	2750	2896	100
2.2561-2.3125	0.1445	123	0.143	2722	2845	100
2.3125-2.3751	0.1964	136	0.1448	2751	2887	100
2.3751-2.4449	0.1929	153	0.1384	2719	2872	100
2.4449-2.5239	0.2221	156	0.146	2753	2909	100
2.5239-2.614	0.1849	166	0.1527	2728	2894	100
2.614-2.7187	0.1646	138	0.1559	2697	2835	100
2.7187-2.8424	0.1894	122	0.14	2764	2886	100
2.8424-2.9922	0.1633	138	0.1434	2758	2896	100
2.9922-3.1797	0.1798	129	0.1468	2748	2877	100
3.1797-3.4251	0.1736	146	0.1389	2736	2882	100
3.4251-3.7696	0.1633	138	0.1426	2738	2876	100
3.7696-4.3147	0.134	135	0.1197	2745	2880	100
4.3147-5.4344	0.1306	144	0.1153	2735	2879	100
5.4344-44.1672	0.1644	163	0.1425	2714	2877	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	1.1512	0.0957	-0.0943	1.2188	0.1837	1.5771	-0.0054	-0.1376	0.0535	0.1236	-0.0256	0.1518	0.038	-0.2449	0.0352	0.0857	-0.0012	0.0055	0.1449	-0.0125	0.1287	29.1276	65.8855	10.8076
2	1.0375	0.1789	0.2214	1.1097	-0.0773	1.4322	-0.0785	-0.1234	0.2352	0.1284	0.0349	0.109	-0.1313	-0.1136	0.0474	0.1188	0.0162	-0.0286	0.111	-0.0313	0.1691	33.7383	75.8107	13.9037
3	5.5196	2.6646	-0.431	9.163	-0.9095	3.7977	-0.2466	0.2907	-0.1906	-0.3937	0.0027	-0.063	0.0556	-0.57	0.2793	0.2395	-0.0654	-0.0474	0.2228	0.0243	0.1663	36.3258	74.1194	-11.6082
4	1.9348	-0.344	0.4377	0.6408	-0.3816	1.2243	-0.0922	0.1257	0.2458	-0.0769	-0.0948	-0.2648	-0.4022	0.332	0.171	0.2236	-0.0612	-0.0306	0.2078	0.0746	0.166	45.6295	81.6654	-9.2925
5	0.7772	-0.2095	0.2285	0.8734	-0.5331	0.957	-0.0678	0.0594	0.1347	-0.0008	-0.0084	-0.0769	-0.1646	0.1127	0.0558	0.1248	-0.032	-0.0263	0.1175	0.016	0.1303	44.0423	72.1402	3.575
6	0.9067	0.565	-1.0059	1.453	-1.4882	2.4387	-0.0147	0.2048	0.3539	0.0462	0.2875	0.3675	-0.3117	-0.5347	-0.2162	0.1975	0.025	-0.0276	0.1738	0.0382	0.2345	31.0627	82.1889	2.2615
7	1.5048	1.2593	-0.4224	2.6564	-0.4141	1.1945	-0.0898	-0.0403	-0.2459	-0.046	0.0591	-0.3929	0.0666	0.4648	0.0376	0.1087	0.0131	0.0147	0.2109	-0.0648	0.1808	64.5944	49.0107	11.712
8	1.3908	0.1809	-0.0975	1.0806	0.3777	1.1929	-0.0577	0.1962	-0.0693	-0.0924	0.0206	-0.0578	0.0655	0.172	0.0144	0.091	0.0117	-0.0002	0.1444	-0.0218	0.098	55.6624	50.5833	9.9617
9	1.1605	0.2513	0.1887	1.5799	-0.1061	1.4354	-0.0594	0.0826	0.0582	-0.0439	0.0242	-0.1621	-0.0602	0.2397	0.0391	0.1031	0.0031	-0.0067	0.1483	-0.0184	0.1259	62.3226	57.4056	17.3509
10	1.6637	0.0932	0.1269	2.0406	0.9206	2.7788	0.039	-0.1528	-0.2542	0.2105	-0.0693	-0.1112	0.1703	-0.1931	0.0487	0.1905	0.015	0.0035	0.1553	0.0027	0.1551	51.147	45.7365	37.3519
11	0.6553	-0.1617	-0.2023	1.023	-0.1707	1.191	-0.0331	-0.0933	0.0798	0.2031	0.0168	0.0033	-0.0611	-0.0152	0.0187	0.1368	0.0056	-0.0159	0.11	-0.0323	0.1032	50.3884	58.201	29.6279
12	0.5053	-0.1253	0.0803	0.8795	-0.15	1.2431	-0.0161	-0.0018	-0.0334	0.0611	0.0178	-0.0476	0.0986	0.0338	0.0015	0.115	0.0114	-0.005	0.0954	-0.0116	0.0972	50.8146	51.1968	23.3835

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 2:48)	A	2 - 48
2	X-RAY DIFFRACTION	2	(chain A and resid 49:83)	A	49 - 83
3	X-RAY DIFFRACTION	3	(chain A and resid 84:90)	A	84 - 90
4	X-RAY DIFFRACTION	4	(chain A and resid 91:108)	A	91 - 108
5	X-RAY DIFFRACTION	5	(chain A and resid 109:185)	A	109 - 185
6	X-RAY DIFFRACTION	6	(chain A and resid 186:199)	A	186 - 199
7	X-RAY DIFFRACTION	7	(chain B and resid 1:9)	B	1 - 9
8	X-RAY DIFFRACTION	8	(chain B and resid 10:48)	B	10 - 48
9	X-RAY DIFFRACTION	9	(chain B and resid 49:83)	B	49 - 83
10	X-RAY DIFFRACTION	10	(chain B and resid 84:101)	B	84 - 101
11	X-RAY DIFFRACTION	11	(chain B and resid 102:147)	B	102 - 147
12	X-RAY DIFFRACTION	12	(chain B and resid 148:199)	B	148 - 199

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