PDB-3mzi: Crystallographic structure of the pseudo-Signaling State of the B...

ID or keywords:

Entry

Database: PDB / ID: 3mzi

Title

Crystallographic structure of the pseudo-Signaling State of the BLUF Photoreceptor PixD (slr1694) Y8F mutant

Components

Activator of photopigment and puc expression

Keywords

PROTEIN BINDING / BLUF (blue-light using FAD) domain / signaling state /

phototaxis

Function / homology

Function and homology information

blue light photoreceptor activity / FAD binding / identical protein binding
Similarity search - Function

Biological species

Synechocystis sp. PCC 6803 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.304 Å

Authors

Yuan, H. / Bauer, C.E.

Citation

Journal: Biochemistry / Year: 2011
Title: Mutational and Structural Studies of the PixD BLUF Output Signal That Affects Light-Regulated Interactions with PixE.
Authors: Yuan, H. / Dragnea, V. / Wu, Q. / Gardner, K.H. / Bauer, C.E.

History

Deposition	May 12, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 31, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 6, 2023	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 / 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_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	3mzi.cif.gz	360.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3mzi.ent.gz	301.5 KB	Display	PDB format
PDBx/mmJSON format	3mzi.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/mz/3mzi ftp://data.pdbj.org/pub/pdb/validation_reports/mz/3mzi	HTTPS FTP

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Related structure data

Related structure data	2hfnS 2hfo S: Starting model for refinement
Similar structure data	1b3k-4 3f5n-5 5onb-3 1quk-d 5onb-2 6fn8-d 5onb-4 2obr-d 5inw-1 3sej-5 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

2hfnS

2hfo

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Activator of photopigment and puc expression

B: Activator of photopigment and puc expression

C: Activator of photopigment and puc expression

D: Activator of photopigment and puc expression

E: Activator of photopigment and puc expression

F: Activator of photopigment and puc expression

hetero molecules

107 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Activator of photopigment and puc expression

B: Activator of photopigment and puc expression

hetero molecules

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

2

C: Activator of photopigment and puc expression

D: Activator of photopigment and puc expression

hetero molecules

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

3

E: Activator of photopigment and puc expression

F: Activator of photopigment and puc expression

hetero molecules

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

Unit cell

Length a, b, c (Å)	41.850, 119.480, 93.260
Angle α, β, γ (deg.)	90.00, 102.89, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Activator of photopigment and puc expression Mass: 17341.738 Da / Num. of mol.: 6 / Mutation: Y8F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Gene: slr1694 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli) / Strain (production host): TunerDE3 / References: UniProt: P74295
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.18 Å³/Da / Density % sol: 43.69 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.1 M (NH4)2SO4, 0.1 M Bis-Tris, 0.01 M Spermidine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24 Å
Detector	Type: NOIR-1 / Detector: CCD / Date: Jan 1, 2005
Radiation	Monochromator: Double crystal 7000 with Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.24 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 37424 / % possible obs: 53.9 % / Observed criterion σ(F): 3.4 / Observed criterion σ(I): 4.5 / Redundancy: 3.7 % / R_merge(I) obs: 0.06 / R_sym value: 0.071 / Net I/σ(I): 13.08
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 1.7 % / R_merge(I) obs: 0.217 / Mean I/σ(I) obs: 4.49 / R_sym value: 0.245 / % possible all: 8

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Processing

Software

Name	Version	Classification
d*TREK		data scaling
PHASER		phasing
PHENIX	(phenix.refine: 1.6_289)	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2HFN; chain A

2hfn

Resolution: 2.304→49.925 Å / Isotropic thermal model: overall / σ(F): 1.99 / Phase error: 25.33 / Stereochemistry target values: TWIN_LSQ_F / Details: twin law "h,-k,-h-l" was used during refinement

	R_factor	Num. reflection	% reflection
R_free	0.2155	1900	5.08 %
R_work	0.1645	-	-
obs	0.1665	37424	94.76 %
all	-	37424	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 55.928 Å² / k_sol: 0.341 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-5.8548 Å²	-0 Å²	0.345 Å²
2-	-	-6.7286 Å²	0 Å²
3-	-	-	-17.396 Å²

Refinement step

Cycle: LAST / Resolution: 2.304→49.925 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6786	0	186	89	7061

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7086
X-RAY DIFFRACTION	f_angle_d	1.241	9636
X-RAY DIFFRACTION	f_dihedral_angle_d	22.956	2646
X-RAY DIFFRACTION	f_chiral_restr	0.081	1068
X-RAY DIFFRACTION	f_plane_restr	0.005	1230

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 (%)
2.304-2.3625	0.3407	67	0.3059	1257	X-RAY DIFFRACTION	45
2.3625-2.4264	0.322	122	0.291	2334	X-RAY DIFFRACTION	83
2.4264-2.4978	0.3104	134	0.2784	2529	X-RAY DIFFRACTION	90
2.4978-2.5784	0.3226	141	0.2648	2696	X-RAY DIFFRACTION	95
2.5784-2.6706	0.3191	140	0.2585	2649	X-RAY DIFFRACTION	95
2.6706-2.7775	0.3174	140	0.2578	2665	X-RAY DIFFRACTION	95
2.7775-2.9039	0.3031	141	0.2442	2675	X-RAY DIFFRACTION	95
2.9039-3.0569	0.3051	138	0.2408	2629	X-RAY DIFFRACTION	95
3.0569-3.2484	0.2494	143	0.2068	2709	X-RAY DIFFRACTION	95
3.2484-3.4991	0.2284	140	0.1811	2655	X-RAY DIFFRACTION	95
3.4991-3.8511	0.2107	140	0.1583	2667	X-RAY DIFFRACTION	94
3.8511-4.408	0.1857	140	0.1182	2658	X-RAY DIFFRACTION	95
4.408-5.552	0.1457	142	0.1005	2697	X-RAY DIFFRACTION	95
5.552-45.4641	0.1485	144	0.1061	2729	X-RAY DIFFRACTION	95

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	2.1379	-0.6191	1.5978	0.8024	-0.9803	1.6152	0.3142	0.1787	-0.2109	-0.4619	-0.2645	0.0417	0.5562	1.0485	0.0226	0.4512	0.3182	0.0068	0.5721	-0.0705	0.2244	-23.4633	47.4032	-108.0241
2	0.4202	-0.0513	-1.0922	0.0335	0.1325	2.943	-0.2523	0.0007	-0.7228	-0.9981	-0.7071	-0.0495	-0.1524	-0.0759	0.9605	1.5168	0.1627	-0.0052	0.7008	0.0302	1.1772	-25.8033	57.1173	-123.1069
3	0.2574	-0.0586	0.5104	0.71	-0.2357	2.4252	0.305	0.4752	-0.1312	0.2786	-0.0275	-0.0873	-0.6314	0.9026	-0.0461	-0.128	0.2957	0.0177	0.5682	0.046	0.35	-21.7509	53.7485	-106.9829
4	0.5657	-0.0402	0.1423	0.0495	-0.2064	1.285	0.1006	0.1728	-0.065	0.0837	0.1339	-0.0208	1.0633	-0.0439	-0.0395	0.7408	0.3582	-0.0309	0.2006	-0.126	0.2905	-27.031	28.2272	-106.3657
5	2.1444	-0.5617	-0.8625	0.1701	0.1121	1.2744	-0.3862	-0.212	-0.2871	0.2063	0.0723	0.2475	0.866	0.2087	0.1788	0.638	0.1243	0.0802	0.3494	0.0251	0.4374	-23.9702	24.2127	-95.9664
6	0.4009	-0.1751	-0.0398	1.7463	0.3621	0.0747	-0.2078	-0.2748	-0.0858	0.4939	0.5673	0.0382	0.5202	0.3431	-0.3518	0.7105	0.1893	0.0516	0.7366	-0.0504	0.1156	-32.9649	26.5776	-89.653
7	0.6026	-0.4209	-1.2356	1.4961	1.0774	2.7001	0.0877	-0.0282	0.1261	0.2895	-0.2089	0.3952	0.3583	0.4875	0.0481	0.1389	0.0693	0.0675	0.4821	-0.1031	0.2011	-48.9554	55.5251	-76.4551
8	3.9818	0.9305	0.2964	3.1598	-0.138	0.1626	-0.4872	1.0981	0.3255	-0.9002	0.0627	0.1679	0.5321	0.0998	0.3687	0.6534	-0.0286	0.0763	0.6507	0.0899	0.3878	-45.5831	65.6241	-85.883
9	2.7165	1.7617	2.2877	1.7472	0.9719	2.491	-0.0394	0.9193	0.0903	0.1943	0.3705	0.203	0.3283	1.2675	-0.3267	0.3831	0.1467	0.073	0.6903	-0.0416	0.2851	-37.7672	58.5482	-89.0521
10	3.2021	0.2314	-1.5873	0.3302	-0.8989	2.7426	-0.0075	1.2582	-0.1158	0.0569	-0.1487	0.0013	-0.2107	-1.3613	0.012	0.2427	0.1835	0.0901	0.9398	0.0951	0.3027	-40.2266	37.8388	-80.2471
11	0.7671	-0.6833	-0.0993	1.5849	0.4885	1.2289	-0.1654	-0.204	-0.1141	-0.0205	-0.1464	-0.0727	0.617	0.036	-0.1004	0.552	0.2446	-0.0342	0.1396	0.0263	0.0305	-51.4088	32.9083	-71.7438
12	1.851	0.8668	-2.9663	0.4019	-1.5121	6.1044	-0.2089	-0.1806	-0.3015	-1.2145	-0.1339	0.2267	1.9682	0.3427	0.1861	0.9842	0.1384	-0.269	0.2738	0.0002	0.3895	-41.0669	27.3785	-73.1507
13	1.884	1.2896	3.8064	1.3391	2.9989	8.0791	0.5707	-0.2217	-0.2007	0.761	-0.1167	-0.1508	1.2547	-1.1518	-0.5036	0.7635	0.1133	-0.0786	0.574	0.0612	0.2083	-38.0144	29.4929	-60.418
14	0.3582	-0.0987	-0.2016	0.3712	-0.4494	2.4164	0.0755	-0.2863	0.0781	-0.2758	0.0312	-0.1214	-1.3883	1.4485	-0.1203	0.6901	-0.1483	0.0411	0.8186	-0.0472	0.1149	-30.1125	63.1509	-43.9519
15	2.4093	-0.5978	1.0197	1.5063	-1.1443	1.0476	0.0045	0.291	-0.0555	0.6935	0.068	-0.0746	-0.5191	0.3184	0.0059	0.6033	-0.0177	-0.0479	0.7161	-0.1667	0.4067	-25.4367	59.9118	-43.3778
16	5.9847	-0.6663	-2.3374	0.4155	0.0359	1.0571	-0.0143	-0.4246	-0.0743	-0.0702	0.4408	-0.0463	0.0294	-0.9207	-0.3666	0.7163	-0.1904	-0.097	1.0577	0.1812	0.6045	-15.1298	54.6131	-55.3386
17	3.0377	0.1426	-1.4135	0.0788	-0.4564	2.7948	0.3658	-0.2121	0.4149	-0.076	-0.2425	-0.0374	-0.0647	0.0597	-0.3262	0.583	0.0104	0.1442	0.4048	0.0639	0.4356	-32.2972	67.3755	-57.3969
18	1.4292	0.5482	-1.4831	0.5798	-0.8159	1.7125	0.1352	-1.1388	0.2262	0.0608	-0.1458	0.097	0.7868	1.6576	0.0231	1.0694	0.0752	0.1146	1.1496	-0.3748	-0.0647	-39.9106	58.9657	-55.9255
19	0.8428	0.9573	-0.3934	1.7719	-0.9284	0.5541	0.2284	0.1484	0.1388	0.6973	-0.0295	0.1266	0.2783	0.1723	-0.0475	0.9876	-0.0393	0.1323	0.1794	0.0029	0.08	-28.2505	61.8071	-59.3515
20	1.4307	-0.4413	1.9469	0.4257	-0.055	4.7601	0.2016	-0.4075	0.1121	0.1288	-0.023	0.1019	0.2464	-0.9205	-0.2282	0.2616	0.1614	-0.1282	0.9807	-0.0304	0.1595	-26.3817	35.9637	-35.5654
21	0.084	-0.0301	-0.0271	1.2126	-0.1537	0.0509	0.2423	-0.0349	0.0217	-0.4282	-0.3771	0.1364	-0.061	0.7939	0.2632	0.3413	0.1062	-0.0555	0.8045	0.0043	0.2788	-34.4651	34.07	-44.6734
22	0.5948	-0.1122	0.2528	1.2068	-1.8362	4.1034	-0.1813	-0.165	0.0727	0.152	-0.2426	-0.3072	-0.2295	0.2814	0.3982	0.1609	0.0993	-0.0804	0.4855	-0.0291	0.1039	-19.774	35.5965	-43.3466

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:15)
2	X-RAY DIFFRACTION	2	(chain A and resid 16:24)
3	X-RAY DIFFRACTION	3	(chain A and resid 25:141)
4	X-RAY DIFFRACTION	4	(chain B and resid 2:80)
5	X-RAY DIFFRACTION	5	(chain B and resid 81:103)
6	X-RAY DIFFRACTION	6	(chain B and resid 104:141)
7	X-RAY DIFFRACTION	7	(chain C and resid 2:90)
8	X-RAY DIFFRACTION	8	(chain C and resid 91:103)
9	X-RAY DIFFRACTION	9	(chain C and resid 104:141)
10	X-RAY DIFFRACTION	10	(chain D and resid 2:6)
11	X-RAY DIFFRACTION	11	(chain D and resid 7:81)
12	X-RAY DIFFRACTION	12	(chain D and resid 82:100)
13	X-RAY DIFFRACTION	13	(chain D and resid 101:141)
14	X-RAY DIFFRACTION	14	(chain E and resid 2:25)
15	X-RAY DIFFRACTION	15	(chain E and resid 26:79)
16	X-RAY DIFFRACTION	16	(chain E and resid 80:87)
17	X-RAY DIFFRACTION	17	(chain E and resid 88:116)
18	X-RAY DIFFRACTION	18	(chain E and resid 117:122)
19	X-RAY DIFFRACTION	19	(chain E and resid 123:141)
20	X-RAY DIFFRACTION	20	(chain F and resid 2:31)
21	X-RAY DIFFRACTION	21	(chain F and resid 32:39)
22	X-RAY DIFFRACTION	22	(chain F and resid 40:141)

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