PDB-6tc7: PAS-GAF bidomain of Glycine max phytochromeA

ID or keywords:

Entry

Database: PDB / ID: 6tc7

Title

PAS-GAF bidomain of Glycine max phytochromeA

Components

Phytochrome

Keywords

PLANT PROTEIN /

phytochrome

Function / homology

Function and homology information

protein-tetrapyrrole linkage / red, far-red light phototransduction / detection of visible light / : / phosphorelay sensor kinase activity /

photoreceptor activity / regulation of DNA-templated transcription / protein homodimerization activity /

nucleus
Similarity search - Function

Biological species

Glycine max (soybean)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.13 Å

Authors

Nagano, S. / Guan, K. / Shenkutie, S.M. / Hughes, J.E.

Funding support

Germany, 1items

Citation

Journal: Nat.Plants / Year: 2020
Title: Structural insights into photoactivation and signalling in plant phytochromes.
Authors: Nagano, S. / Guan, K. / Shenkutie, S.M. / Feiler, C. / Weiss, M. / Kraskov, A. / Buhrke, D. / Hildebrandt, P. / Hughes, J.

History

Deposition	Nov 5, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 6, 2020	Provider: repository / Type: Initial release
Revision 1.1	May 13, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	May 27, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6tc7.cif.gz	249.8 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tc/6tc7 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/6tc7	HTTPS FTP

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Related structure data

Related structure data	6tbySC 6tc5C 6tl4C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6arv-2 2y1x-1 6s7b-1 6arj-1 6s71-1 5dxj-2 5dx1-2 6arj-2 3b3f-2 5dwq-2 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	#183 - Mar 2015 Phototropin similarity (22) #190 - Oct 2015 Two-component Systems similarity (6) #207 - Mar 2017 Photoactive Yellow Protein similarity (4) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (4) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (2) #122 - Feb 2010 Enhanceosome similarity (2) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#183 - Mar 2015
Phototropin
similarity (22)
#190 - Oct 2015
Two-component Systems
similarity (6)
#207 - Mar 2017
Photoactive Yellow Protein
similarity (4)
#152 - Aug 2012
cAMP-dependent Protein Kinase
similarity (4)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (2)
#122 - Feb 2010
Enhanceosome
similarity (2)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (2)

Deposited unit

AAA: Phytochrome

BBB: Phytochrome

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, This PAS-GAF bidomain of Glycine max phyA behaves as monomer in solution. The apparent molecular weight calculated from the elution peak from the gel filtraction ...Evidence: gel filtration, This PAS-GAF bidomain of Glycine max phyA behaves as monomer in solution. The apparent molecular weight calculated from the elution peak from the gel filtraction chromatography corresponds to that of the monomer.

Unit cell

Length a, b, c (Å)	55.423, 113.233, 68.457
Angle α, β, γ (deg.)	90.000, 93.521, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain: (Details: Chains A B) / NCS ensembles : (Details: Chains A and B)

#1: Protein	Phytochrome / Mass: 40026.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Glycine max (soybean) / Gene: phyA, 100790763, GmphyA2, PhyA2, GLYMA_20G090000 / Plasmid: pPROLar.A122 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4YB07
#2: Chemical	ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₃H₄₀N₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.68 Å³/Da / Density % sol: 54.07 %
Crystal grow	Temperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.05 M imidazole, 0.05 M MES, 0.02 M DL-Glutamatic acid monohydrate, 0.02 M DL-Alanine, 0.02M Glycine, 0.02 M DL-Lysine monohydrochloride, 0.02 M DL-Serine, 12% (v/v) Glycerol, 6% (w/v) PEG4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.13→44.35 Å / Num. obs: 46863 / % possible obs: 99.5 % / Redundancy: 6.8 % / B_iso Wilson estimate: 36.395 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.127 / R_pim(I) all: 0.08 / R_rim(I) all: 0.151 / Χ²: 1.02 / Net I/σ(I): 10
Reflection shell	Resolution: 2.13→2.19 Å / Redundancy: 6.9 % / R_merge(I) obs: 1.95 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3828 / CC_1/2: 0.318 / R_pim(I) all: 0.875 / R_rim(I) all: 2.306 / Χ²: 0.98 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0257	refinement
XDS	Mar 15 2019	data reduction
Aimless		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6TBY

6tby

Resolution: 2.13→44.347 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.935 / WR_factor R_free: 0.225 / WR_factor R_work: 0.17 / SU B: 13.657 / SU ML: 0.165 / Average fsc free: 0.8558 / Average fsc work: 0.8671 / Cross valid method: FREE R-VALUE / ESU R: 0.192 / ESU R Free: 0.179
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2415	1866	3.985 %
R_work	0.1892	44964	-
all	0.191	-	-
obs	-	46830	99.399 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 48.593 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.226 Å²	-0 Å²	0.067 Å²
2-	-	-0.05 Å²	-0 Å²
3-	-	-	-0.184 Å²

Refinement step

Cycle: LAST / Resolution: 2.13→44.347 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4982	0	100	176	5258

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.013	5216
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	4954
X-RAY DIFFRACTION	r_angle_refined_deg	2.469	1.664	7072
X-RAY DIFFRACTION	r_angle_other_deg	1.663	1.592	11482
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.109	5	632
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.513	21.93	228
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.163	15	882
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	3.479	15	2
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.255	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.124	0.2	683
X-RAY DIFFRACTION	r_chiral_restr_other	1.141	0.2	24
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	5673
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1037
X-RAY DIFFRACTION	r_nbd_refined	0.234	0.2	994
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	4463
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	2404
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.096	0.2	2502
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.176	0.2	167
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.2	0.2	36
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.153	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	3.705	3.365	2540
X-RAY DIFFRACTION	r_mcbond_other	3.704	3.363	2539
X-RAY DIFFRACTION	r_mcangle_it	5.693	5.007	3165
X-RAY DIFFRACTION	r_mcangle_other	5.692	5.009	3166
X-RAY DIFFRACTION	r_scbond_it	4.856	4.15	2676
X-RAY DIFFRACTION	r_scbond_other	4.855	4.149	2677
X-RAY DIFFRACTION	r_scangle_it	7.249	5.996	3906
X-RAY DIFFRACTION	r_scangle_other	7.249	5.995	3907
X-RAY DIFFRACTION	r_lrange_it	10.14	40.58	5526
X-RAY DIFFRACTION	r_lrange_other	10.131	40.514	5510
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.136	0.05	9246

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.13-2.185	0.307	138	0.331	3297	0.33	3446	0.554	0.553	99.6808	0.328
2.185-2.245	0.351	134	0.315	3218	0.316	3378	0.614	0.635	99.2303	0.308
2.245-2.31	0.337	127	0.298	3096	0.3	3292	0.774	0.779	97.904	0.284
2.31-2.381	0.287	127	0.255	3058	0.256	3189	0.856	0.854	99.8746	0.239
2.381-2.459	0.284	123	0.225	2976	0.227	3101	0.861	0.889	99.9355	0.206
2.459-2.545	0.252	119	0.216	2885	0.218	3009	0.891	0.902	99.8338	0.191
2.545-2.64	0.24	116	0.207	2779	0.208	2900	0.895	0.91	99.8276	0.18
2.64-2.748	0.263	110	0.206	2651	0.208	2777	0.911	0.91	99.4238	0.176
2.748-2.869	0.21	105	0.176	2514	0.178	2647	0.941	0.938	98.9422	0.152
2.869-3.009	0.267	102	0.179	2458	0.183	2562	0.915	0.934	99.9219	0.155
3.009-3.171	0.246	96	0.172	2325	0.174	2427	0.916	0.94	99.7528	0.151
3.171-3.362	0.239	92	0.175	2205	0.177	2300	0.921	0.943	99.8696	0.159
3.362-3.593	0.21	85	0.172	2064	0.173	2172	0.949	0.955	98.9411	0.16
3.593-3.878	0.231	80	0.181	1919	0.183	2015	0.937	0.945	99.206	0.171
3.878-4.245	0.202	74	0.16	1789	0.162	1872	0.944	0.955	99.5192	0.154
4.245-4.741	0.178	66	0.13	1611	0.132	1683	0.959	0.972	99.6435	0.129
4.741-5.464	0.258	59	0.168	1405	0.171	1487	0.941	0.962	98.4533	0.162
5.464-6.667	0.324	50	0.2	1219	0.204	1270	0.931	0.949	99.9213	0.193
6.667-9.324	0.21	40	0.162	946	0.164	1000	0.951	0.954	98.6	0.165
9.324-44.347	0.208	23	0.199	548	0.2	580	0.94	0.943	98.4483	0.217

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	0.0005	0.0007	0.0006	0.0058	-0.0007	0.0016	-0.0023	0.023	0.0066	-0.0352	0.0141	0.0491	0.0027	0.0184	-0.0118	0.2728	0.1183	-0.2313	1.2	0.2848	0.4866	18.2128	16.4119	39.8955
2	3.1671	1.3117	-0.3247	0.5956	0.0748	3.7955	0.0548	0.0638	0.0101	0.1147	0.0171	0.0059	-0.1144	-0.3152	-0.0718	0.2491	0.0058	0.0341	0.1318	-0.0016	0.0553	-2.0249	20.6428	27.9259
3	1.3233	0.0342	0.1277	0.0145	-0.0305	0.4115	0.0677	-0.0251	-0.1733	-0.0076	0.0044	0.0186	-0.0961	0.1385	-0.0721	0.1071	-0.0436	0.0137	0.1762	-0.0149	0.1125	20.3576	12.2544	20.6659
4	1.113	-0.0791	1.8104	1.558	0.4984	3.2031	0.0434	-0.0415	-0.0742	-0.2748	0.0616	0.0249	-0.0626	-0.0823	-0.1051	0.2333	0.15	0.019	0.3015	-0.0467	0.0428	-8.6074	14.0638	-13.9898
5	0.0283	-0.1285	0.0133	1.0455	0.0002	0.823	-0.0301	0.035	-0.0103	0.0828	0.007	-0.0666	0.0119	-0.0206	0.023	0.1555	-0.0256	0.0497	0.1231	-0.0344	0.0783	2.3363	1.7171	-1.5268
6	0.4254	-0.5429	-0.0911	1.4615	-0.2717	0.2201	-0.0147	0.0457	-0.0254	-0.1562	-0.0261	-0.0687	0.0905	-0.0341	0.0409	0.1988	-0.0319	0.0407	0.0989	-0.0556	0.1167	2.9372	-2.8152	-10.1082

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A*	68 - 78
2	X-RAY DIFFRACTION	2	ALL	A*	79 - 150
3	X-RAY DIFFRACTION	3	ALL	A*	151 - 406
4	X-RAY DIFFRACTION	4	ALL	B*	68 - 122
5	X-RAY DIFFRACTION	5	ALL	B*	123 - 272
6	X-RAY DIFFRACTION	6	ALL	B*	273 - 406

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