PDB-5cog: Crystal structure of Yeast IRC4

ID or keywords:

Entry

Database: PDB / ID: 5cog

Title

Crystal structure of Yeast IRC4

Components

IRC4

Keywords

UNKNOWN FUNCTION / DUF1706 /

cell cycle

Function / homology

Function and homology information

mitotic recombination / replication-born double-strand break repair via sister chromatid exchange /

nucleus /

cytoplasm
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.613 Å

Authors

Taylor, J.D. / Matthews, S.J.

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: Structures of the DfsB Protein Family Suggest a Cationic, Helical Sibling Lethal Factor Peptide.
Authors: Taylor, J.D. / Taylor, G. / Hare, S.A. / Matthews, S.J.

History

Deposition	Jul 20, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	Group: Data collection / Database references ...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_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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	5cog.cif.gz	172.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5cog.ent.gz	136.1 KB	Display	PDB format
PDBx/mmJSON format	5cog.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/co/5cog ftp://data.pdbj.org/pub/pdb/validation_reports/co/5cog	HTTPS FTP

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Related structure data

Related structure data	5civSC 5cofC 5comC 5cqvC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4dw7-1 4dve-1 4zra-1 2ql6-16 2jaw-d 5civ-d 5f6x-d 1a3s-d 4dvk-2 4dw5-1 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: IRC4

B: IRC4

hetero molecules

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

1

A: IRC4

hetero molecules

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

2

B: IRC4

hetero molecules

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

Unit cell

Length a, b, c (Å)	146.570, 38.690, 67.100
Angle α, β, γ (deg.)	90.00, 108.59, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-421- HOH
2	1	A-529- HOH
3	1	A-532- HOH

#1: Protein	IRC4 / Increased recombination centers protein 4 Mass: 22959.070 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: IRC4, YDR540C / Plasmid: pQE30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03036
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.36 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 90 mM Sodium nitrate, 90 mM Sodium phosphate dibasic, 90 mM Ammonium sulfate, 0.1 M Sodium HEPES, 0.1 M MOPS, pH 7.5, 12% PEG 550 MME, 6% PEG 20,000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 4, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.61→63.6 Å / Num. obs: 45428 / % possible obs: 97.92 % / Redundancy: 4.2 % / R_merge(I) obs: 0.071 / Net I/σ(I): 9.8
Reflection shell	Resolution: 1.61→1.65 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.576 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 14298 / Num. unique all: 3315 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PHENIX	1.9_1692	phasing
xia2		data scaling
xia2		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5CIV

5civ

Resolution: 1.613→63.599 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 26.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2358	2290	5.04 %
R_work	0.1917	-	-
obs	0.1939	45428	97.92 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.613→63.599 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2851	0	13	653	3517

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2949
X-RAY DIFFRACTION	f_angle_d	0.972	3990
X-RAY DIFFRACTION	f_dihedral_angle_d	12.089	1108
X-RAY DIFFRACTION	f_chiral_restr	0.038	403
X-RAY DIFFRACTION	f_plane_restr	0.005	498

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 (%)
1.6128-1.6479	0.2901	152	0.2584	2662	X-RAY DIFFRACTION	99
1.6479-1.6862	0.3045	130	0.2499	2677	X-RAY DIFFRACTION	97
1.6862-1.7284	0.3102	138	0.2341	2666	X-RAY DIFFRACTION	99
1.7284-1.7751	0.2523	149	0.2249	2620	X-RAY DIFFRACTION	97
1.7751-1.8274	0.2397	142	0.2226	2722	X-RAY DIFFRACTION	99
1.8274-1.8863	0.2969	117	0.2226	2707	X-RAY DIFFRACTION	98
1.8863-1.9538	0.3203	146	0.2285	2662	X-RAY DIFFRACTION	97
1.9538-2.032	0.2789	141	0.2149	2725	X-RAY DIFFRACTION	98
2.032-2.1245	0.2834	163	0.207	2647	X-RAY DIFFRACTION	99
2.1245-2.2365	0.2497	128	0.1984	2728	X-RAY DIFFRACTION	98
2.2365-2.3766	0.2047	141	0.1875	2692	X-RAY DIFFRACTION	98
2.3766-2.5601	0.253	139	0.1848	2724	X-RAY DIFFRACTION	98
2.5601-2.8178	0.2045	155	0.1872	2684	X-RAY DIFFRACTION	97
2.8178-3.2255	0.2202	137	0.1764	2722	X-RAY DIFFRACTION	98
3.2255-4.0637	0.2306	155	0.1516	2715	X-RAY DIFFRACTION	98
4.0637-63.6485	0.178	157	0.1795	2785	X-RAY DIFFRACTION	97

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	0.3808	-0.1905	0.3097	0.1669	0.1768	0.4918	-0.0616	-0.2285	0.2616	0.1303	0.0773	0.1159	-0.043	0.0575	0.0063	0.166	0.0055	-0.0277	0.2072	-0.0117	0.1711	154.0707	-6.5522	28.1885
2	0.2644	0.2214	-0.0028	0.2933	0.147	0.1684	0.0466	0.0201	-0.3425	-0.1198	0.0379	0.4742	0.0224	-0.1551	0.0092	0.1286	0.0151	-0.0315	0.1128	0.0195	0.345	139.0538	-21.5222	18.2059
3	0.4208	0.0001	0.0013	-0.0555	-0.1959	0.2144	0.0002	0.1841	-0.3709	-0.0299	0.0091	0.1708	0.0461	0.0556	-0.0049	0.1121	0.021	-0.0175	0.1248	-0.0099	0.1262	163.0333	-22.2295	20.1118
4	0.6399	-0.2671	0.0245	0.279	-0.0811	0.3115	0.0859	0.4896	-1.2069	0.0614	-0.0192	-0.0903	-0.0611	-0.3588	0.1772	0.1792	0.0077	-0.0572	0.2665	-0.1109	0.3595	154.7956	-25.938	16.5492
5	0.4015	-0.3058	0.0218	0.3556	0.2011	0.1624	-0.046	-0.5265	-0.2757	0.1064	0.0886	0.0495	-0.0076	-0.0576	0.0794	0.1804	0.0255	-0.0135	0.2266	0.0576	0.1247	156.9036	-17.1636	31.5206
6	0.3578	-0.1477	0.0449	0.2764	-0.2552	0.1467	0.0247	0.0041	0.1985	0.0729	0.0215	-0.0752	-0.0115	-0.0177	-0.0069	0.1149	-0.0085	0.0245	0.1933	0.0009	0.1005	173.1149	-9.5877	19.9207
7	0.1826	-0.3561	-0.2444	0.272	0.0213	0.2339	-0.0741	0.0119	0.0161	-0.0229	0.0254	0.0989	-0.0544	0.0194	-0.0083	0.1013	0.0172	-0.0231	0.0946	-0.0031	0.127	148.9735	-11.3912	19.4508
8	0.6984	-0.1289	0.4097	0.5297	0.2702	0.4164	-0.3005	-0.3393	0.404	0.0805	0.0895	0.0674	-0.1524	-0.0053	-0.2016	0.145	0.0272	-0.0479	0.1031	-0.0418	0.1799	144.1379	12.9801	58.7755
9	0.2021	0.0154	0.0724	1.3103	-0.6179	0.5363	0.0324	0.0086	-0.1812	-0.213	0.2427	0.7158	0.048	-0.1084	0.0569	0.1078	-0.012	-0.0048	0.0898	0.0265	0.1999	129.0378	-2.2224	48.591
10	0.1708	-0.0874	-0.0635	-0.0989	-0.1031	0.1707	0.0035	-0.0528	-0.2611	-0.0343	0.0197	-0.032	0.0124	0.0397	0.0001	0.1129	0.0146	-0.0128	0.1077	0.0028	0.1795	149.777	-1.1229	53.2031
11	0.0246	-0.0459	-0.011	0.0197	0.0047	0.0041	-0.2622	0.7184	-0.3058	0.0345	-0.1896	0.0718	0.3963	-0.0004	0	0.255	0.0353	-0.0212	0.4211	-0.0427	0.326	161.4964	-5.7367	49.6235
12	0.0995	-0.0512	0.1427	0.1104	-0.1012	0.25	-0.3506	0.2858	-0.2676	-0.2967	-0.143	0.213	-0.0017	0.3341	-0.0188	0.4153	0.084	0.0006	0.3857	-0.1239	0.2326	153.2713	-4.6227	40.0231
13	1.6669	-0.9094	0.3569	0.6021	-0.1887	0.0992	0.0045	0.2296	-1.0094	0.0021	0.1762	-0.0258	0.0991	0.0017	0.2408	0.1403	-0.0301	-0.0248	0.1533	-0.0979	0.274	143.2044	-7.5562	49.1574
14	0.1241	-0.0853	0.0196	0.154	-0.08	0.1661	-0.045	-0.1425	0.1305	0.1568	0.0455	0.0375	0.1389	0.0952	0.0003	0.1621	0.0376	-0.0038	0.1347	0.0065	0.1352	146.4735	2.0278	62.5561
15	0.124	-0.1118	-0.0934	0.095	0.0485	0.1103	-0.0647	-0.1288	0.3039	0.14	0.0811	0.0394	-0.0068	0.2351	0.0026	0.1025	-0.025	0.0044	0.1738	-0.0166	0.1602	163.8012	9.5217	53.7303
16	0.0447	-0.0072	-0.0312	0.0684	-0.0028	0.0242	-0.0022	0.1759	0.0488	-0.102	0.0127	-0.4167	0.2051	-0.3366	-0.0013	0.1925	-0.0679	0.0289	0.2061	0.0049	0.2353	160.1363	11.0132	44.7586
17	0.2706	-0.4096	0.0025	0.5518	-0.0101	0.1911	-0.1804	0.1232	0.0307	-0.0664	0.0849	0.121	-0.0808	0.0148	-0.0411	0.1037	0.0074	-0.0167	0.0879	-0.0034	0.1584	139.0134	7.9134	50.2541

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 43 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 44 through 79 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 80 through 98 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 99 through 119 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 120 through 141 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 142 through 170 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 2 through 27 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 28 through 43 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 44 through 66 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 67 through 76 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 77 through 82 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 83 through 98 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 99 through 119 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 120 through 136 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 137 through 141 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 142 through 170 )

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