PDB-3nhq: The dark Pfr structure of the photosensory core module of P. aeru...

ID or keywords:

Entry

Database: PDB / ID: 3nhq

Title

The dark Pfr structure of the photosensory core module of P. aeruginosa Bacteriophytochrome

Components

Bacteriophytochrome

Keywords

SIGNALING PROTEIN /

Photoreceptor /

phytochrome / PAS /

signaling

Function / homology

Function and homology information

osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity /

histidine kinase / phosphorelay sensor kinase activity /

photoreceptor activity / regulation of DNA-templated transcription /

ATP binding / identical protein binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Yang, X. / Ren, Z. / Kuk, J. / Moffat, K.

Citation

Journal: Nature / Year: 2011
Title: Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome.
Authors: Yang, X. / Ren, Z. / Kuk, J. / Moffat, K.

History

Deposition	Jun 14, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 30, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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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PDBx/mmCIF format	3nhq.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb3nhq.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	3nhq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nh/3nhq ftp://data.pdbj.org/pub/pdb/validation_reports/nh/3nhq	HTTPS FTP

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Related structure data

Related structure data	3nopC 3notC 3nouC 3c2wS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3c2w-2 3c2w-4 3c2w-3 3c2w-1 2gv9-2 3w9b-d 6a2p-d 1a81-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (19) #190 - Oct 2015 Two-component Systems similarity (7) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (4)

Deposited unit

A: Bacteriophytochrome

B: Bacteriophytochrome

C: Bacteriophytochrome

D: Bacteriophytochrome

E: Bacteriophytochrome

F: Bacteriophytochrome

G: Bacteriophytochrome

H: Bacteriophytochrome

hetero molecules

459 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Bacteriophytochrome

B: Bacteriophytochrome

hetero molecules

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

2

C: Bacteriophytochrome

D: Bacteriophytochrome

hetero molecules

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

3

E: Bacteriophytochrome

F: Bacteriophytochrome

hetero molecules

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

4

G: Bacteriophytochrome

H: Bacteriophytochrome

hetero molecules

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

Unit cell

Length a, b, c (Å)	154.380, 162.979, 436.098
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Bacteriophytochrome / Phytochrome-like protein Mass: 56823.230 Da / Num. of mol.: 8 / Fragment: Photosensory Core Module (UNP Residue 1-497) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: bphP, PA4117 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HWR3
#2: Chemical	ChemComp-BLA / BILIVERDINE IX ALPHA Mass: 582.646 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃₃H₃₄N₄O₆
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.02 Å³/Da / Density % sol: 59.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 7.7 Details: 10mg/ml protein, 0.45 M ammonium phosphate, 0.1 M Tris-HCl, pH 7.7, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 19, 2009 / Details: C(111)
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 2.55→50 Å / Num. all: 188239 / Num. obs: 148709 / % possible obs: 79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / R_merge(I) obs: 0.069 / Net I/σ(I): 23
Reflection shell	Resolution: 2.55→2.59 Å / Redundancy: 2.6 % / R_merge(I) obs: 0.404 / Mean I/σ(I) obs: 1.7 / % possible all: 29.4

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.1_357)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C2W

3c2w

Resolution: 2.55→48.48 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 33.36 / Stereochemistry target values: ML
Details: The refinement was facilitated by an automated real space refinement procedure that optimizes main chain torsional angles. Reference: Haddadian et al. Automated real-space refinement of ...

	R_factor	Num. reflection	% reflection
R_free	0.2579	7389	5.01 %
R_work	0.2152	-	-
obs	0.2174	147602	82.88 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 46.16 Å² / k_sol: 0.317 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	10.2222 Å²	0 Å²	-0 Å²
2-	-	7.17 Å²	0 Å²
3-	-	-	-17.3922 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→48.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30240	0	344	201	30785

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	31298
X-RAY DIFFRACTION	f_angle_d	0.868	42488
X-RAY DIFFRACTION	f_dihedral_angle_d	15.979	11535
X-RAY DIFFRACTION	f_chiral_restr	0.055	4642
X-RAY DIFFRACTION	f_plane_restr	0.003	5565

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 (%)
2.55-2.579	0.3964	87	0.3458	1591	X-RAY DIFFRACTION	29
2.579-2.6093	0.4216	110	0.3386	1872	X-RAY DIFFRACTION	33
2.6093-2.6411	0.3909	119	0.3443	2153	X-RAY DIFFRACTION	39
2.6411-2.6746	0.3681	121	0.3418	2437	X-RAY DIFFRACTION	43
2.6746-2.7098	0.4004	145	0.3332	2672	X-RAY DIFFRACTION	48
2.7098-2.7469	0.3858	140	0.3363	2955	X-RAY DIFFRACTION	52
2.7469-2.7861	0.388	164	0.3316	3290	X-RAY DIFFRACTION	59
2.7861-2.8277	0.401	177	0.3263	3610	X-RAY DIFFRACTION	64
2.8277-2.8719	0.3455	210	0.3101	4079	X-RAY DIFFRACTION	72
2.8719-2.919	0.3838	243	0.3111	4354	X-RAY DIFFRACTION	78
2.919-2.9693	0.4102	246	0.3007	4746	X-RAY DIFFRACTION	85
2.9693-3.0233	0.3399	284	0.2994	5093	X-RAY DIFFRACTION	91
3.0233-3.0814	0.337	279	0.2895	5362	X-RAY DIFFRACTION	96
3.0814-3.1443	0.3639	294	0.279	5565	X-RAY DIFFRACTION	99
3.1443-3.2127	0.3307	288	0.2724	5589	X-RAY DIFFRACTION	100
3.2127-3.2874	0.3231	277	0.2702	5639	X-RAY DIFFRACTION	100
3.2874-3.3696	0.2995	294	0.2632	5585	X-RAY DIFFRACTION	100
3.3696-3.4606	0.276	304	0.2469	5610	X-RAY DIFFRACTION	100
3.4606-3.5624	0.2898	323	0.2354	5604	X-RAY DIFFRACTION	100
3.5624-3.6774	0.2835	308	0.2197	5609	X-RAY DIFFRACTION	100
3.6774-3.8088	0.2755	272	0.21	5625	X-RAY DIFFRACTION	100
3.8088-3.9612	0.2332	286	0.1954	5689	X-RAY DIFFRACTION	100
3.9612-4.1414	0.2062	285	0.1723	5653	X-RAY DIFFRACTION	100
4.1414-4.3596	0.1954	284	0.1521	5642	X-RAY DIFFRACTION	100
4.3596-4.6325	0.1935	312	0.1515	5650	X-RAY DIFFRACTION	100
4.6325-4.9899	0.1999	317	0.1571	5606	X-RAY DIFFRACTION	100
4.9899-5.4914	0.2222	303	0.1702	5688	X-RAY DIFFRACTION	100
5.4914-6.2846	0.232	272	0.1998	5758	X-RAY DIFFRACTION	100
6.2846-7.9124	0.2331	324	0.1916	5710	X-RAY DIFFRACTION	100
7.9124-48.4884	0.1846	321	0.1705	5777	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	-0.078	0.292	-0.3485	0.4296	-0.241	1.9157	0.1194	0.0097	0.006	0.0431	0.0831	0.0163	0.004	-0.0459	-0.1829	0.1609	0.0676	-0.0343	0.254	0.0636	0.2993	-17.7007	17.8672	98.4831
2	0.8693	-0.3076	0.2883	0.9348	0.057	0.8994	0.0776	-0.2069	-0.2599	-0.1175	0.1122	0.3017	0.1707	-0.2837	-0.1983	0.259	-0.1681	-0.1597	0.2869	0.1913	0.3905	-40.1405	-7.82	84.0241
3	0.6148	-0.23	-0.0875	0.8438	0.7155	1.106	-0.0053	-0.0391	0.0883	0.0649	0.1188	-0.0568	0.0015	-0.0173	-0.0834	0.2659	0.0656	-0.0796	0.0993	-0.0087	0.2179	-41.3455	59.928	66.0257
4	0.6543	0.2607	0.1233	0.8094	0.1612	1.0823	0.1394	-0.1685	-0.0488	0.0863	0.0296	0.1723	0.1258	-0.4286	-0.1634	0.3803	-0.0922	-0.1394	0.5159	0.2331	0.4288	-70.6817	36.9765	66.5316
5	0.6953	0.2815	0.192	0.1413	0.1364	2.0292	-0.0374	0.288	0.0337	-0.1218	0.0984	0.081	-0.3333	0.4265	0.0088	0.3695	-0.0819	-0.2056	0.3765	0.1513	0.2764	-49.7394	60.2669	11.1614
6	0.6334	0.0567	0.3879	1.0851	0.4444	1.085	0.1006	0.0506	-0.1175	-0.2354	-0.0364	0.0007	0.1404	-0.085	-0.0591	0.4647	-0.0615	-0.0983	0.2687	0.0456	0.2421	-77.5197	37.9393	21.1216
7	0.4583	0.1056	-0.373	0.9212	-0.0834	1.3888	0.0593	0.0426	0.0007	-0.3072	-0.0247	-0.1052	0.0531	0.0879	-0.0165	0.2689	0.0572	0.075	0.1832	0.0348	0.2068	-12.3259	32.056	45.4875
8	0.4721	0.1019	-0.0784	0.2408	-0.4262	1.3494	0.1346	0.1999	-0.0932	-0.3778	0.0259	-0.0146	0.4273	-0.1803	-0.1447	0.8254	-0.1186	-0.2897	0.3605	0.0638	0.4793	-35.8463	3.8121	39.6799

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H

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