PDB-5uxw: Crystal Structure of Anti-anti-sigma factor PhyR from Bartonella ...

ID or keywords:

Entry

Database: PDB / ID: 5uxw

Title

Crystal Structure of Anti-anti-sigma factor PhyR from Bartonella quintana

Components

Sensory transduction regulatory protein

Keywords

SIGNALING PROTEIN / Bartonella quintana / anti-anti-sigma factor / sensory transduction regulation / two-component response regulation / alphaproteobacteria / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

phosphorelay signal transduction system
Similarity search - Function

Biological species

Bartonella quintana (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Anti-anti-sigma factor PhyR from Bartonella quintana
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Dranow, D.M. / Fairman, J.W. / Lorimer, D. / Edwards, T.E.

History

Deposition	Feb 23, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 28, 2018	Provider: repository / Type: Initial release
Revision 2.0	Feb 6, 2019	Group: Data collection / Other / Polymer sequence / Category: entity_poly / pdbx_SG_project / Item: _entity_poly.pdbx_target_identifier
Revision 2.1	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5uxw.cif.gz	208.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5uxw.ent.gz	166.8 KB	Display	PDB format
PDBx/mmJSON format	5uxw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5uxw_validation.pdf.gz	452.3 KB	Display	wwPDB validaton report
Full document	5uxw_full_validation.pdf.gz	453.5 KB	Display
Data in XML	5uxw_validation.xml.gz	20.1 KB	Display
Data in CIF	5uxw_validation.cif.gz	28.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ux/5uxw ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5uxw	HTTPS FTP

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Related structure data

Related structure data	4qicS 4x03 PDB Unreleased entry 5uxv 5uxx S: Starting model for refinement
Similar structure data	6uk1-4 6uk1-3 5zz4-6 1snu-1 3n1q-3 4i84-1 6uk1-2 6tfp-5 2pzf-2 5ot9-2 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
Other databases	TargetTrack: SSGCID-BAQUA.17156.A

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#190 - Oct 2015 Two-component Systems similarity (5) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Sensory transduction regulatory protein

B: Sensory transduction regulatory protein

hetero molecules

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

1

A: Sensory transduction regulatory protein

hetero molecules

defined by author
Evidence: gel filtration
31.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Sensory transduction regulatory protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	119.770, 120.980, 83.280
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

#1: Protein	Sensory transduction regulatory protein Mass: 30976.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella quintana (bacteria) / Strain: Toulouse / Gene: BQ10980 / Plasmid: BAQUA.17156.A.CB1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3LUV4
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.43 Å³/Da / Density % sol: 49.48 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: JCSG+(H11): 25% PEG-3350, 100MM BIS -TRIS/HCL, PH=5.5, 200MM MGCL2 , CRYO PROTECTED WITH 20% EG; BAQUA.17156.A.CB1.PS02157 AT 9.1 MG/ML, TRAY 257812 PH range: 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 12, 2014 / Details: BERYLLIUM LENSES
Radiation	Monochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.3→48.94 Å / Num. obs: 26897 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / B_iso Wilson estimate: 24.02 Å² / R_merge(I) obs: 0.136 / Net I/σ(I): 10.94
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.596 / Mean I/σ(I) obs: 2.74 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX	dev_2666	refinement
XSCALE		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4QIC

4qic

Resolution: 2.3→48.94 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.15

	R_factor	Num. reflection	% reflection
R_free	0.235	1371	5.1 %
R_work	0.181	-	-
obs	0.184	26887	98.7 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 30.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→48.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3753	0	28	177	3958

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3918
X-RAY DIFFRACTION	f_angle_d	0.937	5330
X-RAY DIFFRACTION	f_dihedral_angle_d	12.889	1447
X-RAY DIFFRACTION	f_chiral_restr	0.033	632
X-RAY DIFFRACTION	f_plane_restr	0.004	692

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 (%)
2.3-2.3822	0.3351	122	0.2343	2543	X-RAY DIFFRACTION	99
2.3822-2.4775	0.2912	132	0.2266	2520	X-RAY DIFFRACTION	99
2.4775-2.5903	0.2876	130	0.2175	2537	X-RAY DIFFRACTION	99
2.5903-2.7269	0.2782	155	0.2109	2502	X-RAY DIFFRACTION	99
2.7269-2.8977	0.2548	126	0.2071	2557	X-RAY DIFFRACTION	99
2.8977-3.1214	0.2566	137	0.1986	2545	X-RAY DIFFRACTION	99
3.1214-3.4354	0.2626	116	0.1828	2572	X-RAY DIFFRACTION	99
3.4354-3.9324	0.2179	161	0.1565	2529	X-RAY DIFFRACTION	99
3.9324-4.9536	0.1754	129	0.1422	2597	X-RAY DIFFRACTION	98
4.9536-48.9531	0.1921	163	0.1612	2614	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	4.5836	-1.2279	0.1098	4.6404	-0.7968	5.3848	0.1452	-0.0303	-0.4272	-0.1545	-0.0951	-0.1015	0.0474	0.2353	-0.021	0.2105	0.0181	0.0053	0.1726	-0.0079	0.2063	35.4307	-8.7339	20.3102
2	2.5851	-0.2589	0.2603	2.7601	-0.4505	3.4927	0.0572	-0.324	-0.7537	0.0557	-0.1309	0.0511	0.21	0.0317	0.0468	0.2172	0.0201	-0.0036	0.232	0.0404	0.3449	30.7734	-14.6767	22.7167
3	4.436	0.4837	0.2494	4.4631	-0.7794	6.2611	0.0232	0.1258	-0.3727	-0.2837	-0.1352	0.6322	0.1269	-0.3226	0.1347	0.1925	0.0512	0.0053	0.1388	-0.0213	0.3056	22.603	-5.8228	15.4462
4	0.8932	1.0747	-0.2559	3.729	0.4735	1.5506	0.2504	0.6797	-0.6257	-0.8285	-0.3186	0.7598	0.1131	-0.1689	0.0868	0.3654	0.1207	-0.1154	0.385	-0.1571	0.3998	19.5704	-7.4765	7.1702
5	5.5111	4.741	3.4797	7.2319	-0.0797	4.7315	0.0043	-0.0359	0.3624	0.3131	-0.3228	-0.1027	-0.3538	0.4286	0.2945	0.2095	0.028	-0.0027	0.1922	0.0177	0.1412	28.6292	16.8902	15.0034
6	6.7519	1.8257	-0.0579	3.2953	-0.4241	0.028	-0.3443	0.3073	0.1026	-0.266	0.1004	-0.2123	-0.3849	0.2403	0.2324	0.2961	-0.0445	-0.0011	0.374	0.0625	0.1837	31.5024	18.38	9.2132
7	3.6982	4.039	-2.7181	9.0568	-0.2382	3.7147	0.9562	-0.6159	0.6382	0.7607	-0.7907	0.5097	-0.4952	0.6029	-0.2303	0.5356	-0.0365	-0.0306	0.354	-0.0261	0.4637	31.0062	25.5228	23.6118
8	7.2859	-2.7689	1.3386	6.573	0.2211	6.2293	0.0378	0.6634	0.4804	0.165	-0.0534	-0.4513	-0.4153	0.6018	-0.0095	0.3256	-0.0605	0.0036	0.1268	-0.0182	0.1997	35.1579	16.5054	20.72
9	4.2295	-0.231	0.0568	4.6472	0.7337	2.4589	0.1089	-0.1607	-0.1152	0.2597	-0.0517	-0.2671	-0.0908	0.2091	-0.0713	0.1989	-0.0388	0.0059	0.2338	-0.0044	0.1226	35.4822	7.919	22.5078
10	2.8485	0.6878	-1.3412	3.8198	0.802	7.9246	0.181	0.2044	-0.046	0.1601	0.0101	0.2239	-0.2385	-0.4549	-0.1742	0.2138	0.0598	0.0167	0.15	0.0188	0.1999	20.4483	6.6628	18.43
11	3.5724	-0.7158	1.5349	2.0061	0.1888	2.5121	-0.0694	-0.0917	0.1181	-0.0817	0.005	0.3671	-0.1019	-0.3241	0.0642	0.184	0.0214	-0.0173	0.2298	0.032	0.2145	-14.257	33.14	-0.2455
12	4.1766	-1.1567	-1.2587	4.5298	0.2106	5.1885	0.0057	-0.0211	-0.2831	0.094	-0.1121	0.1278	0.3817	-0.3767	0.1018	0.1296	0.0051	0.0142	0.1938	0.0243	0.1554	-6.1378	24.0616	5.8059
13	5.8495	-0.926	-0.8915	3.6351	-1.3819	2.1523	-0.1575	-0.1815	-0.3988	0.0947	0.085	0.3819	0.116	-0.2983	0.0931	0.2699	-0.0171	0.0175	0.2845	0.0456	0.169	-7.9479	21.2978	14.3049
14	4.4606	3.2618	-1.154	7.9613	-1.1147	3.3319	0.1076	-0.3346	0.1587	0.5155	-0.1859	-0.0062	-0.2788	0.325	0.0822	0.1506	0.0045	-0.0353	0.2183	0.0121	0.1867	15.7467	33.7538	9.3411
15	6.6031	3.2925	-2.5558	5.7412	-1.7876	7.2733	0.1639	0.2783	-0.0184	-0.0937	-0.0585	-0.5022	-0.2646	0.2499	-0.0151	0.1614	0.025	0.0041	0.2869	0.0438	0.2364	22.686	35.3887	0.6308
16	5.0667	-0.2605	-0.0932	3.9523	-0.0199	5.2425	0.0228	0.7581	0.2335	-0.5949	-0.0826	-0.188	-0.1919	-0.2626	0.1154	0.3304	-0.0542	0.036	0.2688	0.0574	0.1911	13.2646	37.0574	-3.405
17	3.5097	-0.5128	1.503	4.3693	-1.1974	3.2813	-0.0048	0.1522	-0.0081	-0.0519	0.0609	0.0174	-0.2586	0.0373	-0.0362	0.1293	0.0035	0.0378	0.2342	0.0136	0.1724	3.7387	31.9504	1.4895

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 2 THROUGH 22 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 23 THROUGH 64 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 65 THROUGH 108 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 109 THROUGH 136 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 137 THROUGH 148 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 149 THROUGH 172 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 173 THROUGH 183 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 184 THROUGH 199 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 200 THROUGH 242 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 243 THROUGH 266 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 2 THROUGH 64 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 65 THROUGH 108 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 109 THROUGH 135 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 136 THROUGH 162 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 163 THROUGH 183 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 184 THROUGH 219 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 220 THROUGH 265 )

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