PDB-3qpt: Crystal structure of the Salmonella transcriptional regulator SlyA

ID or keywords:

Entry

Database: PDB / ID: 3qpt

Title

Crystal structure of the Salmonella transcriptional regulator SlyA

Components

Transcriptional regulator slyA

Keywords

TRANSCRIPTION / MarR/SlyA protein family / winged helix-turn-helix / transcriptonal regulator

Function / homology

Function and homology information

response to stress / DNA-binding transcription factor activity / regulation of DNA-templated transcription /

Biological species

Salmonella enterica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.4 Å

Authors

Dolan, K.T. / Duguid, E.M.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Crystal Structures of SlyA Protein, a Master Virulence Regulator of Salmonella, in Free and DNA-bound States.
Authors: Dolan, K.T. / Duguid, E.M. / He, C.

History

Deposition	Feb 14, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3qpt.cif.gz	66 KB	Display	PDBx/mmCIF format
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Validation report

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

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Related structure data

Related structure data	3q5fC C: citing same article (ref.)
Similar structure data	3vb2-d 2rh0-2 4aih-2 6j7z-d 2jhn-1 6c5u-2 4aih-3 5iqb-4 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Transcriptional regulator slyA

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

1

A: Transcriptional regulator slyA

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

Unit cell

Length a, b, c (Å)	50.686, 50.686, 173.584
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

#1: Protein	Transcriptional regulator slyA / Cytolysin slyA / Salmolysin Mass: 16902.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica (bacteria) / Strain: subsp. enterica serovar Typhimurium / Gene: slyA, STM1444 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40676
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	AUTHORS STATE THAT THE SEQUENCING EXPERIMENTS OF THE CLONES CONFIRMED THE CODING SEQUENCE AT THESE ...AUTHORS STATE THAT THE SEQUENCING EXPERIMENTS OF THE CLONES CONFIRMED THE CODING SEQUENCE AT THESE POSITIONS IS GAGCCG (CORRESPONDING TO GLU-PRO).

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.9 Å³/Da / Density % sol: 35.4 %

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Data collection

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Relative weight: 1

Reflection

Redundancy: 10.9 % / Av σ(I) over netI: 34.04 / Number: 71740 / R_merge(I) obs: 0.097 / Χ²: 1.81 / D res high: 2.25 Å / D res low: 50 Å / Num. obs: 6601 / % possible obs: 95.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.1	50	97.1	1	0.05	4.009	10.9
4.85	6.1	100	1	0.068	3.493	12.9
4.23	4.85	100	1	0.061	3.43	13.4
3.85	4.23	100	1	0.08	3.047	13.6
3.57	3.85	100	1	0.09	2.193	14.1
3.36	3.57	100	1	0.107	1.673	14.3
3.19	3.36	99.7	1	0.133	1.464	14.7
3.05	3.19	100	1	0.17	1.197	14.3
2.94	3.05	100	1	0.225	1.099	14.3
2.83	2.94	100	1	0.234	0.992	13.4
2.75	2.83	100	1	0.26	0.865	12.3
2.67	2.75	100	1	0.277	0.867	11.1
2.6	2.67	100	1	0.334	0.833	10.3
2.53	2.6	100	1	0.342	0.837	9
2.48	2.53	96.8	1	0.358	0.77	7.3
2.42	2.48	96.3	1	0.386	0.736	6.5
2.38	2.42	90.8	1	0.41	0.847	5.2
2.33	2.38	81.1	1	0.493	0.804	4.8
2.29	2.33	74.5	1	0.464	0.966	4
2.25	2.29	66.1	1	0.404	1.207	3.3

Reflection

Resolution: 2.2→50 Å / Num. obs: 6928 / % possible obs: 94 % / Redundancy: 10.8 % / R_merge(I) obs: 0.096 / Net I/σ(I): 11.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
2.2-2.24	3.3	0.713	1	58.2
2.24-2.28	4	0.4	1	63.9
2.28-2.32	4.4	0.496	1	78
2.32-2.37	5	0.496	1	88.1
2.37-2.42	6.2	0.41	1	90.4
2.42-2.48	7.2	0.401	1	97.4
2.48-2.54	8.3	0.364	1	100
2.54-2.61	9.8	0.321	1	100
2.61-2.69	11.2	0.324	1	100
2.69-2.77	11.9	0.263	1	100
2.77-2.87	12.9	0.253	1	100
2.87-2.99	14	0.231	1	100
2.99-3.12	14.5	0.204	1	100
3.12-3.29	14.5	0.146	1	100
3.29-3.49	14.5	0.116	1	100
3.49-3.76	14.2	0.094	1	100
3.76-4.14	13.8	0.08	1	100
4.14-4.74	13.3	0.062	1	100
4.74-5.97	13.1	0.066	1	100
5.97-50	11	0.05	1	97.5

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Phasing

Phasing

Method:

SAD

Phasing MAD

D res high: 2.25 Å / D res low: 42.56 Å / FOM : 0.636 / FOM acentric: 0.672 / FOM centric: 0.564 / Reflection: 6544 / Reflection acentric: 4383 / Reflection centric: 1862

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
7.99-42.56	0.653	0.758	0.603	200	64	136
5.7-7.99	0.665	0.801	0.515	305	160	145
4.67-5.7	0.749	0.801	0.669	368	223	145
4.05-4.67	0.693	0.742	0.593	431	287	144
3.62-4.05	0.685	0.742	0.559	462	319	143
3.31-3.62	0.622	0.649	0.556	531	377	154
3.07-3.31	0.63	0.673	0.516	555	404	151
2.87-3.07	0.651	0.681	0.557	582	443	139
2.71-2.87	0.653	0.665	0.619	631	473	158
2.57-2.71	0.639	0.648	0.605	647	498	139
2.45-2.57	0.614	0.637	0.536	669	477	143
2.34-2.45	0.577	0.604	0.51	640	401	142
2.25-2.34	0.526	0.545	0.476	523	257	123

Phasing dm

FOM : 0.76 / FOM acentric: 0.77 / FOM centric: 0.73 / Reflection: 6547 / Reflection acentric: 4685 / Reflection centric: 1862

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
2.3-2.4	0.62	0.64	0.56	952	738	214
2.4-2.8	0.71	0.72	0.66	1978	1533	445
2.8-3.2	0.76	0.79	0.68	1135	844	291
3.2-4	0.83	0.85	0.79	1153	820	333
4-6.4	0.87	0.91	0.8	974	604	370

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
RESOLVE	2.15	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2.4→39.17 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.911 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 22.383 / SU ML: 0.22 / SU R Cruickshank DPI: 0.5865 / Cross valid method: THROUGHOUT / ESU R: 0.581 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27126	255	4.5 %	RANDOM
R_work	0.23583	-	-	-
obs	0.23736	5435	99.56 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 48.853 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.92 Å²	0.96 Å²	0 Å²
2-	-	1.92 Å²	0 Å²
3-	-	-	-2.88 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→39.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1065	0	0	16	1081

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	1092
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.771	1.987	1476
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.344	5	134
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.168	24.468	47
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.989	15	226
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.057	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	179
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	772
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.689	1.5	664
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.403	2	1081
X-RAY DIFFRACTION	r_scbond_it	2.57	3	428
X-RAY DIFFRACTION	r_scangle_it	4.392	4.5	393
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.26	14	-
R_work	0.277	353	-
obs	-	-	94.83 %

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	6.5239	1.1438	-10.2154	1.5966	2.9842	32.6612	-0.9537	0.0514	-0.7931	-0.4403	-0.066	-0.1816	0.7857	-0.1906	1.0197	0.3459	0.0924	0.0581	0.1297	-0.0039	0.1442	17.2186	-3.5454	3.8528
2	3.8129	-3.5698	3.6673	5.0892	-1.2223	7.5919	0.1727	0.2026	-0.0665	-0.0276	-0.0864	-0.1298	-0.1469	0.4093	-0.0863	0.1836	-0.0197	-0.0933	0.0614	-0.0127	0.0632	7.144	5.8636	12.7546
3	4.9132	-0.3685	-1.3283	4.7757	3.4002	10.6122	-0.0743	0.1025	0.1463	-0.1129	0.0387	0.3691	-0.5701	-0.3167	0.0356	0.1242	0.0405	-0.0134	0.0584	0.0109	0.0742	-0.6113	11.2051	3.9789
4	14.3854	-6.8684	3.2057	7.3605	-1.8435	7.0352	-0.2005	-0.4404	1.1503	0.2761	0.2548	-0.2474	-0.9607	-0.1602	-0.0542	0.2373	-0.0517	-0.024	0.0707	0.001	0.1896	7.4302	14.661	14.0615
5	3.8402	-0.3647	2.8358	0.7029	1.3297	9.2253	-0.3044	0.2469	0.5041	-0.0679	-0.0069	-0.2276	-0.6996	0.7965	0.3113	0.2345	-0.0473	0.0197	0.3334	-0.0067	0.4466	27.3453	4.897	-2.9635

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 22
2	X-RAY DIFFRACTION	2	A	23 - 46
3	X-RAY DIFFRACTION	3	A	47 - 80
4	X-RAY DIFFRACTION	4	A	88 - 115
5	X-RAY DIFFRACTION	5	A	116 - 143

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