PDB-4i6g: a vertebrate cryptochrome with FAD

ID or keywords:

Entry

Database: PDB / ID: 4i6g

Title

a vertebrate cryptochrome with FAD

Components

Cryptochrome-2

Keywords

TRANSCRIPTION / Cryptochrome / Circadian Clock / Metabolite / Photolyase fold / FAD / Fbxl3 / Periods / Nucleus

Function / homology

Function and homology information

regulation of sodium-dependent phosphate transport / Cry-Per complex / negative regulation of glucocorticoid secretion / negative regulation of glucocorticoid receptor signaling pathway / negative regulation of circadian rhythm / lipid storage / entrainment of circadian clock by photoperiod / photoreceptor activity / response to light stimulus / phosphatase binding ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Xing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N.

Citation

Journal: Nature / Year: 2013
Title: SCFFBXL3 ubiquitin ligase targets cryptochromes at their cofactor pocket.
Authors: Xing, W. / Busino, L. / Hinds, T.R. / Marionni, S.T. / Saifee, N.H. / Bush, M.F. / Pagano, M. / Zheng, N.

History

Deposition	Nov 29, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2013	Group: Database references
Revision 1.2	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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4i6g.cif.gz	416.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4i6g.ent.gz	343.4 KB	Display	PDB format
PDBx/mmJSON format	4i6g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4i6g_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	4i6g_full_validation.pdf.gz	1.2 MB	Display
Data in XML	4i6g_validation.xml.gz	39.5 KB	Display
Data in CIF	4i6g_validation.cif.gz	54.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i6/4i6g ftp://data.pdbj.org/pub/pdb/validation_reports/i6/4i6g	HTTPS FTP

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Related structure data

Related structure data	4i6eC 4i6jC C: citing same article (ref.)
Similar structure data	5xtq-1 4eg2-3 6d0z-d 6orm-d 6tg0-d 5dg8-d 6fn3-d 5ze4-d 6kx8-1 6q02-d 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
Related items in Molecule of the Month	#91 - Jul 2007 Thymine Dimers similarity (8)

Deposited unit

A: Cryptochrome-2

B: Cryptochrome-2

hetero molecules

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

1

A: Cryptochrome-2

hetero molecules

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

2

B: Cryptochrome-2

hetero molecules

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

Unit cell

Length a, b, c (Å)	97.525, 97.525, 128.821
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	78
Space group name H-M	P4₃

#1: Protein	Cryptochrome-2 Mass: 58689.047 Da / Num. of mol.: 2 / Fragment: UNP residues 1-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cry2, Kiaa0658 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9R194
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.61 Å³/Da / Density % sol: 52.87 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES-imadzole, pH 6.5, 7.2% PEG8000, 20% ethylene glyco(v/v), 0.03M NaF,NaBr,NaI, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 28, 2011
Radiation	Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 60952 / Num. obs: 60952 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / R_merge(I) obs: 0.058 / R_sym value: 0.058 / Net I/σ(I): 37.22
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.53 / Mean I/σ(I) obs: 2.475 / R_sym value: 0.53 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHENIX	(phenix.refine: 1.8.1_1168)	model building
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX	1.8.1_1168	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→43.615 Å / SU ML: 0.28 / σ(F): 1.36 / Phase error: 26.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2384	2003	3.29 %
R_work	0.1973	-	-
obs	0.1987	60952	99.9 %
all	-	60952	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→43.615 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7740	0	106	263	8109

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	8080
X-RAY DIFFRACTION	f_angle_d	1.151	10983
X-RAY DIFFRACTION	f_dihedral_angle_d	15.869	2971
X-RAY DIFFRACTION	f_chiral_restr	0.081	1136
X-RAY DIFFRACTION	f_plane_restr	0.005	1401

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 (%)
2.2-2.255	0.3244	140	0.2558	4167	X-RAY DIFFRACTION	99
2.255-2.316	0.3204	140	0.2416	4195	X-RAY DIFFRACTION	100
2.316-2.3841	0.279	140	0.2304	4224	X-RAY DIFFRACTION	100
2.3841-2.4611	0.2723	142	0.2219	4220	X-RAY DIFFRACTION	100
2.4611-2.549	0.2425	143	0.2098	4176	X-RAY DIFFRACTION	100
2.549-2.6511	0.2807	141	0.2166	4212	X-RAY DIFFRACTION	100
2.6511-2.7717	0.2515	141	0.2137	4200	X-RAY DIFFRACTION	100
2.7717-2.9178	0.2995	140	0.2121	4201	X-RAY DIFFRACTION	100
2.9178-3.1006	0.2865	144	0.2087	4211	X-RAY DIFFRACTION	100
3.1006-3.3399	0.2619	143	0.2087	4218	X-RAY DIFFRACTION	100
3.3399-3.6759	0.2182	147	0.1902	4219	X-RAY DIFFRACTION	100
3.6759-4.2074	0.225	145	0.1716	4226	X-RAY DIFFRACTION	100
4.2074-5.2994	0.1982	148	0.1744	4225	X-RAY DIFFRACTION	100
5.2994-43.6231	0.2193	149	0.1992	4255	X-RAY DIFFRACTION	99

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	3.8224	-0.0905	1.461	5.0363	0.5993	2.5783	-0.4117	0.0218	-0.7084	-0.4512	0.1217	0.409	1.1433	-0.1776	0.0863	0.931	-0.1386	0.2919	0.3896	-0.0392	0.6043	25.4751	-36.792	2.1535
2	3.2791	2.8858	0.06	5.4831	0.4853	2.779	-0.3725	0.2431	-0.6272	-0.414	0.1894	-0.2569	1.0442	0.2461	0.1876	0.7698	0.0297	0.252	0.3742	-0.0005	0.3687	35.3584	-27.3529	-4.6835
3	1.155	-0.9432	0.0991	5.4706	2.1814	2.1193	-0.3141	0.4905	-0.4521	-0.5819	0.0099	0.5886	0.5166	-0.4062	0.3202	0.8034	-0.2984	0.1166	0.5765	-0.1209	0.6741	16.4939	-28.974	-1.3613
4	4.8342	-2.0927	1.2095	2.1732	-1.3377	3.2741	-0.3708	-0.4047	-0.5233	0.4989	0.0244	0.5376	0.4318	-0.2182	0.3683	0.5329	-0.1413	0.2184	0.413	-0.0844	0.6087	14.5393	-19.9075	17.0494
5	2.6339	0.3914	1.3792	5.8397	0.2638	0.7466	-0.6773	0.3409	-1.4408	-0.2686	0.0927	-1.2046	1.634	0.1896	0.4824	1.4831	0.0361	0.4209	0.8814	-0.1232	1.5989	35.9615	-43.9391	-3.2208
6	0.5761	-0.2787	-0.624	1.4148	-0.0823	5.9111	-0.0688	-0.1099	-0.1355	-0.1625	-0.0838	-0.7203	0.5536	0.8714	0.1436	0.5637	0.1674	0.1829	0.7716	0.0879	0.5122	44.1742	-20.2986	-2.4221
7	8.6147	-1.1853	-3.5794	7.0361	2.0706	6.5036	0.7042	-0.9996	0.5155	1.7977	-0.0664	-0.8485	-0.0561	1.1854	-0.1939	0.7682	0.0857	-0.0621	0.7689	0.2797	0.407	38.2507	-24.3845	17.488
8	0.463	-0.354	0.0017	0.2585	-0.0152	-0.0039	0.2399	-0.1542	0.2663	1.1411	-0.9093	-1.5398	0.4674	-1.3219	0.3522	1.4453	-0.5583	-0.2034	1.2502	0.3619	0.889	41.7579	-11.8507	18.3465
9	5.0647	-0.1002	-1.5052	3.6343	0.6642	6.2674	-0.0522	-0.9544	-0.0295	0.4837	-0.1403	0.064	0.5457	0.2105	0.2565	0.6174	-0.0803	0.104	0.589	0.08	0.4264	27.024	-21.8297	22.14
10	3.0998	0.2264	0.7084	4.792	0.3703	1.8196	-0.1548	0.4042	0.1131	-0.4635	-0.0331	0.5891	0.137	-0.4874	0.2406	0.3988	-0.0665	0.0554	0.4282	-0.0367	0.5057	17.7038	-5.6262	2.9672
11	4.9885	-1.1962	0.1249	4.4686	1.292	2.5255	0.1647	0.0286	0.3661	-0.0244	-0.0429	-0.1392	-0.3813	0.3988	-0.1057	0.2717	-0.0775	0.0425	0.2334	0.008	0.1448	37.1357	0.314	5.3214
12	3.3124	1.212	0.2984	5.3202	-0.9012	1.8127	-0.0277	0.1791	0.3315	0.0994	0.0231	0.8682	0.1804	-0.3649	-0.059	0.3011	-0.0413	0.0165	0.3387	0.0321	0.3132	24.9539	-2.7851	4.2915
13	4.1692	-1.4419	-0.2525	6.288	-1.2029	6.013	0.1973	-0.5683	0.4767	0.5195	-0.4003	0.8111	0.0975	-0.7754	0.4125	0.5915	-0.1736	0.1216	0.5959	-0.1492	0.5142	30.9855	6.0981	16.5462
14	3.8148	2.433	-0.1307	5.221	-0.5997	1.8234	0.2872	-0.4069	0.6159	0.1566	-0.1729	-1.3381	-0.5966	0.816	-0.0954	0.4508	-0.2069	0.0384	0.6145	-0.1094	0.6777	50.5119	9.2774	10.8606
15	8.18	-0.0018	-0.1444	4.3356	0.8183	6.4007	0.0241	-0.1233	1.2658	-0.842	-0.16	0.3965	-1.2834	-1.0867	-0.0355	0.6684	0.0436	0.0493	0.3857	-0.005	0.6386	24.9229	14.0805	6.5758
16	1.7264	-1.4907	-1.0608	4.4596	1.032	0.7295	-0.213	-1.5132	-1.7088	0.8144	-0.6154	0.3854	1.0785	0.0074	0.4424	0.7361	-0.2174	0.2239	0.7442	0.0458	1.0199	29.3705	-11.4999	12.7036
17	1.4704	0.4159	0.1108	1.3609	-0.5986	0.1825	-0.3946	0.5187	0.7224	-0.7369	-0.478	1.2108	-0.7647	-1.3749	0.0394	0.1331	0.2436	-0.2164	1.3566	-0.4792	1.0734	15.8173	17.8327	32.4926
18	5.1679	-1.6484	0.7666	2.3534	0.7826	0.8803	-0.1817	-0.0226	-0.6385	-0.0503	-0.3042	1.2278	0.2941	-1.1628	0.1907	0.3583	-0.1126	-0.0614	0.9567	-0.2674	0.7439	19.7869	9.9301	30.9978
19	0.8146	-1.2014	-0.0499	1.9574	-0.0255	0.1911	-0.3413	0.4696	0.1908	-1.1984	-0.183	0.5922	-0.302	-0.715	-0.2785	0.7358	0.4549	-0.4459	1.2003	-0.264	1.4462	15.8573	25.0979	28.0944
20	4.1503	-0.2635	-0.5763	0.0777	0.0056	0.0917	0.0473	-0.0466	0.1587	0.0466	0.0731	0.5987	-0.203	-0.3412	-0.0794	0.7096	0.8522	-0.9359	1.1596	-0.3078	1.7688	12.8969	31.7211	25.6446
21	2.0965	0.9604	0.325	3.1728	0.2047	0.857	0.196	0.0961	0.7771	0.608	-0.1535	0.299	-0.1085	-0.3968	-0.0307	0.6381	0.257	-0.0817	0.8519	-0.3626	1.1715	27.6608	33.6291	47.8605
22	7.4875	0.0476	-0.5025	2.6975	-2.4188	2.3461	0.971	0.0403	-0.2286	-0.0415	0.4689	1.0081	-0.0222	-1.1712	-1.1564	0.675	-0.0017	-0.0819	1.5078	-0.082	1.4967	5.4737	10.113	33.5487
23	2.5441	2.1876	-1.2882	2.5879	1.1222	8.6842	-0.617	0.3287	-0.13	0.2078	-0.2751	0.3063	0.6194	-1.0307	0.7275	0.6824	-0.3059	0.1043	0.7126	-0.1829	0.4792	29.2481	1.8987	26.0976
24	4.7164	-1.0012	-2.8618	3.2251	1.7287	2.7614	-0.2828	-0.6536	-0.0589	1.0239	0.026	0.1434	0.4654	-0.5201	0.2994	0.6635	0.0008	0.0575	0.7547	-0.0796	0.5023	28.5002	11.1489	47.8253
25	1.3576	-0.7912	0.5409	2.2512	1.0779	4.7302	0.5507	-1.2097	-0.3261	1.5267	-0.6061	0.8161	0.0986	-0.4173	-0.0021	1.058	-0.0575	0.1795	1.4521	-0.3612	0.8116	28.7002	21.1505	62.8378
26	5.5689	0.0023	0.0404	1.7067	0.8455	2.5228	-0.2267	0.3688	1.1696	-0.3756	-0.0352	0.0139	-0.8271	-0.4496	0.1363	0.5995	0.1391	-0.1055	0.5	-0.1284	0.9657	41.4472	31.0093	35.9091
27	5.1865	0.6609	0.7058	5.5143	0.31	4.0448	0.1362	-0.0209	-0.0471	0.173	0.3209	-0.6571	0.2921	0.2512	-0.411	0.308	0.0642	-0.0775	0.3477	-0.1315	0.3173	49.6674	11.6642	36.9547
28	3.3498	-0.6497	-1.8581	4.4737	0.0812	3.7799	-0.0971	-0.4577	1.3771	-0.3671	0.2473	0.0339	-0.7332	-0.2305	-0.0997	0.3334	0.0649	-0.0251	0.3145	-0.1138	0.5109	45.5036	23.3602	36.7206
29	3.5743	0.5174	-0.0637	0.9134	1.0319	3.8609	-0.0685	-0.6462	-0.2939	0.8821	0.4368	-0.9605	0.3476	0.2853	-0.3695	0.6959	0.2108	-0.3264	0.5149	-0.1452	0.6008	56.7482	6.9152	45.5433
30	2.4689	-3.6338	-0.9634	6.1311	-0.3946	3.5349	0.3112	-0.0727	0.2972	-0.2267	0.2053	-1.3316	0.0985	1.2848	-0.103	0.3896	0.1946	-0.1653	0.7312	-0.3314	0.8446	65.1506	7.9139	37.0274
31	5.3952	0.2206	1.4713	8.0684	-3.6668	2.65	-1.0441	-0.0875	1.9661	0.7225	0.0592	-0.8904	-1.6962	0.2211	0.676	1.1954	-0.1827	-0.1445	0.9024	-0.2132	1.479	58.907	37.8887	38.8507
32	8.5722	-0.7318	0.8086	3.719	3.2291	3.0404	0.1038	-1.0601	-0.1179	1.6649	-0.0136	1.1512	0.4339	-0.5821	0.1472	1.121	0.4964	-0.1229	0.9349	-0.1611	1.0604	37.5746	17.9445	45.6296

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 21:52)
2	X-RAY DIFFRACTION	2	(chain A and resid 53:101)
3	X-RAY DIFFRACTION	3	(chain A and resid 102:162)
4	X-RAY DIFFRACTION	4	(chain A and resid 163:189)
5	X-RAY DIFFRACTION	5	(chain A and resid 190:209)
6	X-RAY DIFFRACTION	6	(chain A and resid 210:232)
7	X-RAY DIFFRACTION	7	(chain A and resid 233:243)
8	X-RAY DIFFRACTION	8	(chain A and resid 244:268)
9	X-RAY DIFFRACTION	9	(chain A and resid 269:307)
10	X-RAY DIFFRACTION	10	(chain A and resid 308:341)
11	X-RAY DIFFRACTION	11	(chain A and resid 342:383)
12	X-RAY DIFFRACTION	12	(chain A and resid 384:425)
13	X-RAY DIFFRACTION	13	(chain A and resid 426:440)
14	X-RAY DIFFRACTION	14	(chain A and resid 441:483)
15	X-RAY DIFFRACTION	15	(chain A and resid 484:511)
16	X-RAY DIFFRACTION	16	(chain A and resid 900:900)
17	X-RAY DIFFRACTION	17	(chain B and resid 21:64)
18	X-RAY DIFFRACTION	18	(chain B and resid 65:101)
19	X-RAY DIFFRACTION	19	(chain B and resid 102:127)
20	X-RAY DIFFRACTION	20	(chain B and resid 128:141)
21	X-RAY DIFFRACTION	21	(chain B and resid 142:184)
22	X-RAY DIFFRACTION	22	(chain B and resid 185:208)
23	X-RAY DIFFRACTION	23	(chain B and resid 209:226)
24	X-RAY DIFFRACTION	24	(chain B and resid 227:286)
25	X-RAY DIFFRACTION	25	(chain B and resid 287:308)
26	X-RAY DIFFRACTION	26	(chain B and resid 309:340)
27	X-RAY DIFFRACTION	27	(chain B and resid 341:382)
28	X-RAY DIFFRACTION	28	(chain B and resid 383:425)
29	X-RAY DIFFRACTION	29	(chain B and resid 426:467)
30	X-RAY DIFFRACTION	30	(chain B and resid 468:500)
31	X-RAY DIFFRACTION	31	(chain B and resid 501:511)
32	X-RAY DIFFRACTION	32	(chain B and resid 900:900)

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