PDB-4hh3: Structure of the AppA-PpsR2 core complex from Rb. sphaeroides

ID or keywords:

Entry

Database: PDB / ID: 4hh3

Title

Structure of the AppA-PpsR2 core complex from Rb. sphaeroides

Components

AppA protein
Transcriptional regulator, PpsRTranscriptional regulation

Keywords

FLAVOPROTEIN/TRANSCRIPTION /

helix bundle / SCHIC domain /

PAS domain / AppA-PpsR complex / FLAVOPROTEIN-TRANSCRIPTION complex

Function / homology

Function and homology information

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

Biological species

Rhodobacter sphaeroides (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 Å

Authors

Winkler, A. / Heintz, U. / Lindner, R. / Reinstein, J. / Shoeman, R. / Schlichting, I.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2013
Title: A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression.
Authors: Winkler, A. / Heintz, U. / Lindner, R. / Reinstein, J. / Shoeman, R.L. / Schlichting, I.

History

Deposition	Oct 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 5, 2013	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2013	Group: Database references
Revision 1.2	Jul 17, 2013	Group: Database references
Revision 1.3	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4hh3.cif.gz	299.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4hh3.ent.gz	243.7 KB	Display	PDB format
PDBx/mmJSON format	4hh3.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hh/4hh3 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/4hh3	HTTPS FTP

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Related structure data

Related structure data	4hh0C 4hh1C 4hh2C C: citing same article (ref.)
Similar structure data	6nha-d 5dnf-d 5e24-1 4hab-d 3vxo-d 7byy-d 3sjd-d 2x0s-d 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 (1) #207 - Mar 2017 Photoactive Yellow Protein similarity (1)

Deposited unit

A: Transcriptional regulator, PpsR

B: Transcriptional regulator, PpsR

C: AppA protein

83.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	89.780, 188.300, 51.860
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Transcriptional regulator, PpsR / Transcriptional regulation Mass: 28835.143 Da / Num. of mol.: 2 / Fragment: UNP residues 2-257 Source method: isolated from a genetically manipulated source Details: TEV cleavable N-term His tag / Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: ppsR, RHOS4_18870, RSP_0282 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q3J179
#2: Protein	AppA protein Mass: 25480.275 Da / Num. of mol.: 1 / Fragment: UNP residues 168-399 / Mutation: C399S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: appA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q53119
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.64 Å³/Da / Density % sol: 53.34 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES, 64 mM tri-sodium citrate, 10% PEG 5000 monomethyl ether, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99981 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2012 / Details: Dynamically bendable mirror
Radiation	Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99981 Å / Relative weight: 1
Reflection	Resolution: 1.75→50 Å / Num. all: 89653 / Num. obs: 89594 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / B_iso Wilson estimate: 28.1 Å² / R_merge(I) obs: 0.0053 / Net I/σ(I): 20.3
Reflection shell	Resolution: 1.75→1.85 Å / Redundancy: 8.5 % / R_merge(I) obs: 0.684 / Mean I/σ(I) obs: 2.85 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.75→44.907 Å / SU ML: 0.18 / Isotropic thermal model: isotropic / σ(F): 2 / Phase error: 19.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.198	4489	5.01 %
R_work	0.1699	-	-
obs	0.1713	89590	99.94 %
all	-	89653	-

Solvent computation

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

Displacement parameters

B_iso mean: 31.2 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→44.907 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5447	0	0	683	6130

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5632
X-RAY DIFFRACTION	f_angle_d	1.022	7658
X-RAY DIFFRACTION	f_dihedral_angle_d	13	2186
X-RAY DIFFRACTION	f_chiral_restr	0.068	912
X-RAY DIFFRACTION	f_plane_restr	0.005	1007

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 (%)
1.75-1.7699	0.2661	161	0.2384	2776	X-RAY DIFFRACTION	100
1.7699-1.7907	0.2599	146	0.238	2843	X-RAY DIFFRACTION	100
1.7907-1.8126	0.2763	153	0.2239	2744	X-RAY DIFFRACTION	100
1.8126-1.8355	0.2781	159	0.2112	2808	X-RAY DIFFRACTION	100
1.8355-1.8597	0.2354	136	0.2067	2822	X-RAY DIFFRACTION	100
1.8597-1.8851	0.2351	149	0.1939	2790	X-RAY DIFFRACTION	100
1.8851-1.9121	0.2436	169	0.1953	2785	X-RAY DIFFRACTION	100
1.9121-1.9406	0.2188	141	0.1908	2782	X-RAY DIFFRACTION	100
1.9406-1.9709	0.2306	132	0.1968	2829	X-RAY DIFFRACTION	100
1.9709-2.0033	0.2604	167	0.1986	2817	X-RAY DIFFRACTION	100
2.0033-2.0378	0.2306	151	0.1816	2756	X-RAY DIFFRACTION	100
2.0378-2.0749	0.1986	128	0.1757	2895	X-RAY DIFFRACTION	100
2.0749-2.1148	0.2401	163	0.1716	2757	X-RAY DIFFRACTION	100
2.1148-2.1579	0.2044	144	0.1701	2847	X-RAY DIFFRACTION	100
2.1579-2.2048	0.226	121	0.1677	2821	X-RAY DIFFRACTION	100
2.2048-2.2561	0.205	149	0.167	2822	X-RAY DIFFRACTION	100
2.2561-2.3126	0.1872	149	0.1662	2800	X-RAY DIFFRACTION	100
2.3126-2.3751	0.244	162	0.1694	2833	X-RAY DIFFRACTION	100
2.3751-2.445	0.1898	153	0.1758	2820	X-RAY DIFFRACTION	100
2.445-2.5239	0.223	144	0.1848	2839	X-RAY DIFFRACTION	100
2.5239-2.6141	0.2258	150	0.1763	2821	X-RAY DIFFRACTION	100
2.6141-2.7187	0.2204	147	0.1727	2879	X-RAY DIFFRACTION	100
2.7187-2.8424	0.1873	150	0.1724	2805	X-RAY DIFFRACTION	100
2.8424-2.9923	0.2091	154	0.1713	2855	X-RAY DIFFRACTION	100
2.9923-3.1797	0.1839	147	0.1672	2842	X-RAY DIFFRACTION	100
3.1797-3.4251	0.1801	152	0.1638	2909	X-RAY DIFFRACTION	100
3.4251-3.7696	0.1848	150	0.1559	2867	X-RAY DIFFRACTION	100
3.7696-4.3147	0.1648	154	0.1511	2917	X-RAY DIFFRACTION	100
4.3147-5.4346	0.1614	153	0.1466	2925	X-RAY DIFFRACTION	100
5.4346-44.9213	0.1904	155	0.1808	3095	X-RAY DIFFRACTION	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	3.1724	-0.3951	-1.2127	2.8413	0.323	1.6603	0.2068	0.5818	0.1223	-0.6147	-0.2816	-0.9043	0.1612	0.2116	0.3165	0.2145	0.0639	0.2302	0.2766	0.1917	0.5052	48.9996	30.3299	17.4896
2	0.3003	-0.7727	0.0274	3.2435	-0.7549	0.4649	0.0327	-0.0856	-0.0718	-0.0871	-0.0142	0.3199	0.0578	-0.0219	-0.0166	0.1118	0.0048	-0.0109	0.1484	0.0049	0.1098	33.7056	74.6173	4.6997
3	2.2536	-0.5964	-1.3834	5.0457	0.4302	2.9739	-0.1086	-0.2054	-0.2166	0.1159	-0.0292	0.4609	-0.0138	-0.1649	0.0728	0.1786	0.0324	0.0211	0.1418	-0.0146	0.2302	23.7519	97.1137	7.6798
4	4.1389	-0.3914	-1.5812	1.1849	-0.6512	2.412	-0.0504	-0.1329	-0.1616	-0.0062	-0.0625	-0.2051	0.075	0.0637	0.0349	0.1381	-0.0279	0.0256	0.1386	0.0348	0.2014	31.9236	25.06	32.8015
5	0.5585	-1.0106	0.8695	2.0934	-1.2631	1.3956	-0.0805	-0.2405	-0.1544	0.1445	0.1391	0.204	0.0007	-0.1304	-0.091	0.1613	0.0109	0.0405	0.2289	0.0183	0.2267	29.9808	70.1241	3.6144
6	3.2045	-0.8552	1.3777	2.0352	-0.0927	4.054	-0.0846	0.4731	0.2289	-0.11	-0.0995	-0.1408	-0.0002	0.2868	0.1444	0.172	0.013	0.01	0.2204	0.0525	0.1978	30.4273	82.8832	-20.6247
7	2.6935	-0.0934	-0.2595	1.7759	-0.1253	1.3152	-0.1406	-0.468	-0.2277	0.2456	0.0719	0.0256	-0.0434	-0.1114	0.0537	0.1639	0.0222	0.0069	0.2505	0.0368	0.06	48.6134	63.6948	21.2417
8	2.7315	0.019	-0.8118	1.9043	-0.2924	2.9388	-0.0259	0.4227	-0.0294	-0.3709	-0.0912	-0.2251	0.3332	0.0501	0.0954	0.235	0.0153	0.0157	0.2193	0.0321	0.0288	53.6287	64.0033	-1.8353

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 120 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 121 through 176 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 177 through 257 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 5 through 120 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 121 through 176 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 177 through 257 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 184 through 263 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 264 through 400)

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