PDB-8sbf: Full-length structure of the LysR-type transcriptional regulator,...

ID or keywords:

Entry

Database: PDB / ID: 8sbf

Title

Full-length structure of the LysR-type transcriptional regulator, ACIAD0746, from Acinetobacter baylyi

Components

Putative transcriptional regulator (LysR family)

Keywords

DNA BINDING PROTEIN / LysR-type / LTTR / transcriptional regulator / cysteine biosynthesis / sulfur metabolism / sulfite

Function / homology

Function and homology information

transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function

Biological species

Acinetobacter baylyi ADP1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.29 Å

Authors

Momany, C. / Nune, M. / Brondani, J.C. / Afful, D. / Neidle, E. / Galloway, N.R.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: FinR, a LysR-type transcriptional regulator involved in sulfur homeostasis with homologs in diverse microorganisms
Authors: Momany, C. / Nune, M. / Brondani, J.C. / Afful, D. / Neidle, E. / Galloway, N.R.

History

Deposition	Apr 3, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sbf.cif.gz	833.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8sbf.ent.gz	584.9 KB	Display	PDB format
PDBx/mmJSON format	8sbf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8sbf_validation.pdf.gz	470.1 KB	Display	wwPDB validaton report
Full document	8sbf_full_validation.pdf.gz	483.9 KB	Display
Data in XML	8sbf_validation.xml.gz	48.6 KB	Display
Data in CIF	8sbf_validation.cif.gz	68.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sb/8sbf ftp://data.pdbj.org/pub/pdb/validation_reports/sb/8sbf	HTTPS FTP

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Related structure data

Related structure data	8sbhC C: citing same article (ref.)
Similar structure data	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: Putative transcriptional regulator (LysR family)

C: Putative transcriptional regulator (LysR family)

B: Putative transcriptional regulator (LysR family)

D: Putative transcriptional regulator (LysR family)

hetero molecules

134 kDa, 4 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)	106.597, 109.690, 110.268
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Putative transcriptional regulator (LysR family) Mass: 33478.625 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Polyhistidine purification tag added to C-terminus / Source: (gene. exp.) Acinetobacter baylyi ADP1 (bacteria) / Gene: ACIAD0746 / Plasmid: pET28b(+).SapKO-CH.ACIAD0746 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6FE56
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Na
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50.04 %
Crystal grow	Temperature: 297 K / Method: microbatch / pH: 7.5 Details: ACIAD0746 was dialyzed against 20 mM TRIS, 500 mM NaCl, 10 mM mercaptolethanol, 10% glycerol, pH 8. 2 microL protein was mixed with 2 microL Hampton Research HR-CSI-23 (0.2 M MgCl2, 0.1 M ...Details: ACIAD0746 was dialyzed against 20 mM TRIS, 500 mM NaCl, 10 mM mercaptolethanol, 10% glycerol, pH 8. 2 microL protein was mixed with 2 microL Hampton Research HR-CSI-23 (0.2 M MgCl2, 0.1 M HEPES pH 7.5, 30% v/v PEG 400)

Crystal

Density Matthews: 2.46 Å³/Da / Density % sol: 50.04 %

Crystal grow

Temperature: 297 K / Method: microbatch / pH: 7.5
Details: ACIAD0746 was dialyzed against 20 mM TRIS, 500 mM NaCl, 10 mM mercaptolethanol, 10% glycerol, pH 8. 2 microL protein was mixed with 2 microL Hampton Research HR-CSI-23 (0.2 M MgCl2, 0.1 M ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: RAYONIX MX300-HS / Detector: CCD / Date: Jun 28, 2012 / Details: Insertion device

Radiation

Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.29→100 Å / Num. obs: 57811 / % possible obs: 99.1 % / Redundancy: 6.6 % / B_iso Wilson estimate: 46.3 Å² / R_merge(I) obs: 0.047 / Χ²: 1.582 / Net I/av σ(I): 45.9 / Net I/σ(I): 19.1

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	Χ²	Diffraction-ID	% possible all
2.294-2.34	4.9	0.403	2799	1.479	1	98
2.34-2.38	5.8	0.363	2840	1.374	1	98.9
2.38-2.43	6.3	0.284	2889	1.251	1	99.8
2.43-2.48	6.8	0.235	2872	1.039	1	100
2.48-2.53	6.9	0.217	2866	1.162	1	100
2.53-2.59	6.8	0.185	2894	1.175	1	100
2.59-2.66	6.8	0.173	2892	1.325	1	99.9
2.66-2.73	6.6	0.165	2869	1.807	1	99.9
2.73-2.81	6.9	0.106	2875	1.196	1	99.8
2.81-2.9	6.9	0.09	2914	1.201	1	99.9
2.9-3	6.9	0.073	2880	1.156	1	99.8
3-3.12	6.9	0.058	2895	1.213	1	99.8
3.12-3.26	6.9	0.05	2895	1.345	1	99.6
3.26-3.44	6.9	0.047	2896	1.663	1	99.5
3.44-3.65	6.7	0.045	2888	1.984	1	99.6
3.65-3.93	6.6	0.043	2935	2.379	1	99.2
3.93-4.33	6.8	0.039	2892	2.239	1	99.1
4.33-4.96	6.7	0.041	2927	2.755	1	99
4.96-6.24	6.7	0.038	2946	2.396	1	98.4
6.24-100	6.4	0.02	2947	1.451	1	93.4

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.29→26.45 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7333
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2576	2912	5.05 %
R_work	0.2114	54791	-
obs	0.2138	57703	98.74 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 69.37 Å²

Refinement step

Cycle: LAST / Resolution: 2.29→26.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9169	0	25	584	9778

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0022	9382
X-RAY DIFFRACTION	f_angle_d	0.5208	12718
X-RAY DIFFRACTION	f_chiral_restr	0.0395	1473
X-RAY DIFFRACTION	f_plane_restr	0.0045	1670
X-RAY DIFFRACTION	f_dihedral_angle_d	15.5848	3527

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 (%)
2.29-2.33	0.3733	124	0.3176	2304	X-RAY DIFFRACTION	89.04
2.33-2.37	0.353	119	0.2952	2582	X-RAY DIFFRACTION	98.43
2.37-2.42	0.3389	138	0.2849	2600	X-RAY DIFFRACTION	99.46
2.42-2.46	0.3295	142	0.2776	2588	X-RAY DIFFRACTION	100
2.46-2.51	0.3668	159	0.2686	2610	X-RAY DIFFRACTION	99.96
2.51-2.57	0.3599	121	0.2706	2623	X-RAY DIFFRACTION	99.93
2.57-2.63	0.315	120	0.2547	2631	X-RAY DIFFRACTION	99.96
2.63-2.69	0.3158	157	0.2682	2600	X-RAY DIFFRACTION	99.71
2.69-2.76	0.287	161	0.2448	2574	X-RAY DIFFRACTION	99.78
2.76-2.85	0.3096	125	0.2469	2628	X-RAY DIFFRACTION	99.82
2.85-2.94	0.2971	140	0.2546	2638	X-RAY DIFFRACTION	99.86
2.94-3.04	0.3167	142	0.2559	2627	X-RAY DIFFRACTION	99.71
3.04-3.16	0.2877	142	0.2312	2606	X-RAY DIFFRACTION	99.71
3.16-3.31	0.3054	148	0.2222	2631	X-RAY DIFFRACTION	99.78
3.31-3.48	0.2716	131	0.219	2630	X-RAY DIFFRACTION	99.32
3.48-3.7	0.227	139	0.1971	2640	X-RAY DIFFRACTION	99.25
3.7-3.98	0.2264	139	0.1772	2612	X-RAY DIFFRACTION	99.17
3.98-4.38	0.2102	134	0.1699	2684	X-RAY DIFFRACTION	99.23
4.38-5.01	0.1995	159	0.1639	2629	X-RAY DIFFRACTION	98.9
5.01-6.3	0.2546	150	0.1995	2662	X-RAY DIFFRACTION	98.29
6.3-26.45	0.2119	122	0.1963	2692	X-RAY DIFFRACTION	94.49

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	4.51591011097	1.62809674784	0.0257707078472	7.62253910965	3.59823277909	6.14851232595	0.15282661826	-0.0696812288084	-0.216917774717	0.255082497401	-0.206773180704	-0.0433111262642	0.0239870964693	0.0625287037243	0.00577571150855	0.310936534998	-0.0211799068003	0.0206387734244	0.35320148071	0.0715645115949	0.231896158361	-26.3401621592	21.4159388203	-43.3016433905
2	3.79459771466	-0.511902953368	2.50854248459	2.09751313817	-2.28278823753	8.08440354667	-0.189928219758	0.0501686700294	0.112179772128	0.125519548847	0.109816376723	0.175214596056	-0.593508907812	0.306683092556	0.0799558018955	0.363737802013	0.0114597901712	0.0318840557713	0.251911759709	-0.00789261756637	0.35825385959	-31.2586909868	18.34115282	-9.33797893426
3	8.4821513705	-1.75570718599	1.72880470802	5.01803219328	0.728056318946	4.00229652863	-0.185434200767	-0.424147417592	-0.377062033524	0.53514496298	0.205840870455	-0.206061337494	0.828588071485	0.601168807375	-0.0756014116396	0.526258208797	0.157573894698	0.0923035639697	0.417309557463	0.00737369518325	0.257887011204	8.55727918787	-22.8867069583	11.393883958
4	5.48848082138	-4.37347550114	4.27899835108	2.15631083601	-3.32047892579	5.00118158309	0.544293004496	0.491419030322	-0.596287471252	-0.259542609204	-0.138500644888	0.468040486839	0.401993886028	0.164973394061	-0.402295084707	0.41174793319	-0.0496664691068	-0.156304595753	0.378962954699	0.0451950058651	0.54771993392	-39.1907068246	-1.60623889705	-19.856152497
5	4.06598616886	0.223539794688	-1.83382483428	4.80722154166	2.37509497759	5.7447416862	0.0999415482913	0.525017020364	0.293289544907	-0.511520432438	-0.049278869493	0.161644309345	-0.320019882701	-0.285687516166	-0.044892599247	0.368449318959	0.115422826918	-0.0352666581354	0.253544758844	0.00835542033493	0.278708943518	-0.639538778387	-12.7094131359	-7.25986615521
6	2.52381053821	0.925454170277	0.187861497929	9.35106486343	-4.10276226695	3.45556024673	0.371758055753	-0.218841871729	-0.263916477671	-0.0397349838132	-0.609346799866	0.181194513992	-0.152905230794	0.63070141753	0.255158298888	0.564416683342	0.0780218441119	0.125168068692	0.514293172555	0.0569266660986	0.461190298541	1.26834114351	16.8747905206	-5.6090538699
7	2.24439534561	0.815880855966	-0.318573915285	9.78911108209	-5.23444875209	4.56735087964	0.0589163016417	-0.042638485782	0.241239950836	1.01452813267	-0.0087235668442	0.687910713013	-0.765546911938	0.261809663807	-0.0364081442424	0.428031557537	-0.0598398732991	0.0717677842672	0.400254425157	-0.0474077834592	0.390134589659	-2.423923762	25.5845853985	-8.40957443319
8	9.42989563884	-1.8354505437	1.31498926638	5.85193313532	0.0706463640504	4.87559918586	-0.378429702072	0.560948117166	0.363377540019	-0.624526529607	0.0174133719866	1.23183708572	-1.34489859207	-0.169937304246	0.263521652286	0.887988980907	-0.0660505405459	-0.201928415244	0.349786846667	0.0238288725274	0.675182943334	-36.16363076	39.8073573733	-53.6348436397
9	5.29610667904	-1.70145611832	0.807849142422	3.12295454103	-2.20940514942	5.40381939714	-0.367590109694	-0.695980672658	-1.21678981658	-0.239046659276	-0.380355280205	-0.230930104066	1.14264826248	1.43038829885	0.547918494598	0.680406982003	0.329147742749	0.263912209534	0.874889156224	0.466372480823	0.808521895157	11.6340748789	13.873056335	-26.024025434

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 85 )	A	A	1 - 85	1 - 85
2	2	chain 'A' and (resid 86 through 294 )	A	A	86 - 294	86 - 294
3	3	chain 'C' and (resid 1 through 85 )	C	B	1 - 85	1 - 85
4	4	chain 'C' and (resid 86 through 295 )	C	B	86 - 295	86 - 295
5	5	chain 'B' and (resid 1 through 85 )	B	C	1 - 85	1 - 85
6	6	chain 'B' and (resid 86 through 187 )	B	C	86 - 187	86 - 187
7	7	chain 'B' and (resid 188 through 295 )	B	C	188 - 295	188 - 295
8	8	chain 'D' and (resid 1 through 85 )	D	G	1 - 85	1 - 85
9	9	chain 'D' and (resid 86 through 293 )	D	G	86 - 293	86 - 293

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