PDB-9guj: Crystal structure of transcription factor NtcA from Synechococcus...

ID or keywords:

Entry

Database: PDB / ID: 9guj

Title

Crystal structure of transcription factor NtcA from Synechococcus elongatus in complex with its transcriptional co- activator PipX and its target DNA (Crystal II)

Components

DNA
Global nitrogen regulator
PipX

Keywords

DNA BINDING PROTEIN / DNA binding protein. Transcriptional regulation / NtcA / nitrogen regulation / cyanobacteria / CRP / PipX

Function / homology

Function and homology information

DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function

Biological species

Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 4.3 Å

Authors

Llacer, J.L. / Forcada-Nadal, A. / Rubio, V.

Funding support

Spain, 2items

Citation

Journal: Nucleic Acids Res. / Year: 2025
Title: Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase.
Authors: Forcada-Nadal, A. / Bibak, S. / Salinas, P. / Contreras, A. / Rubio, V. / Llacer, J.L.

History

Deposition	Sep 19, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 12, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9guj.cif.gz	583.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9guj.ent.gz	477.6 KB	Display	PDB format
PDBx/mmJSON format	9guj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gu/9guj ftp://data.pdbj.org/pub/pdb/validation_reports/gu/9guj	HTTPS FTP

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Related structure data

Related structure data	9gquC 9gugC 9guhC 9guiC 9gukC 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
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (12) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (2) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (5) #241 - Jan 2020 Twenty Years of Molecules similarity (1) #251 - Nov 2020 Adenylyl Cyclase similarity (5) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1)

PDB pages

PDBj /

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NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
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Deposited unit

D: Global nitrogen regulator

F: Global nitrogen regulator

G: DNA

I: DNA

J: PipX

H: PipX

A: Global nitrogen regulator

B: Global nitrogen regulator

C: DNA

E: DNA

K: PipX

hetero molecules

169 kDa, 11 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	165.710, 165.710, 177.550
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	79
Space group name H-M	I4

#1: Protein	Global nitrogen regulator Mass: 24862.053 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Gene: ntcA, Synpcc7942_0127 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P29283
#2: DNA chain	DNA Mass: 9219.000 Da / Num. of mol.: 4 / Source method: obtained synthetically Source: (synth.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
#3: Protein	PipX Mass: 10540.987 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria) Gene: Synpcc7942_2061 / Plasmid: pTrc99A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q7X386
#4: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID Mass: 146.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₆O₅ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.6 Å³/Da / Density % sol: 65.87 %
Crystal grow	Temperature: 294.15 K / Method: vapor diffusion, sitting drop Details: PipX-NtcA-DNA complex was in 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate and 10mM 2-oxoglutarate. CRYSTALLIZATION ...Details: PipX-NtcA-DNA complex was in 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate and 10mM 2-oxoglutarate. CRYSTALLIZATION SOLUTION: 0,1M Tris-HCL pH 8,5, 2M ammonium phosphate and 0,1M ZnCl2. Cryo protectant: 4M KCL

Crystal

Density Matthews: 3.6 Å³/Da / Density % sol: 65.87 %

Crystal grow

Temperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: PipX-NtcA-DNA complex was in 50 mM sodium citrate pH 6.5, 0.5 M NaCl, 5 mM magnesium cloride, 50 mM arginine hydrocloride, 50 mM Na L-glutamate and 10mM 2-oxoglutarate. CRYSTALLIZATION ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9772 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9772 Å / Relative weight: 1
Reflection	Resolution: 4.3→82.9 Å / Num. obs: 16116 / % possible obs: 98.5 % / Redundancy: 3.8 % / R_sym value: 0.074 / Net I/σ(I): 4.8
Reflection shell	Resolution: 4.3→4.53 Å / Num. unique obs: 16116 / R_sym value: 0.472

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0352	refinement
SCALA		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 4.3→82.86 Å / Cor.coef. F_o:F_c: 0.867 / Cor.coef. F_o:F_c free: 0.853 / SU B: 160.368 / SU ML: 0.966 / Cross valid method: THROUGHOUT / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.31614	802	5 %	RANDOM
R_work	0.28357	-	-	-
obs	0.28528	15313	98.46 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 91.929 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	35.59 Å²	0 Å²	-0 Å²
2-	-	35.59 Å²	-0 Å²
3-	-	-	-71.18 Å²

Refinement step

Cycle: 1 / Resolution: 4.3→82.86 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8809	2419	40	0	11268

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.011	11751
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	9891
X-RAY DIFFRACTION	r_angle_refined_deg	1.614	1.684	16374
X-RAY DIFFRACTION	r_angle_other_deg	0.447	1.547	23029
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.763	5	1096
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.128	5	89
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.64	10	1606
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	1883
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	11594
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2222
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
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 4.3→4.411 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.383	73	-
R_work	0.311	1109	-
obs	-	-	98.91 %

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	1.8913	-0.2085	0.3793	3.0115	-1.7348	5.2134	-0.0238	0.53	-0.0251	-0.398	0.1335	0.3466	-0.0989	-0.2741	-0.1097	0.1851	0.1173	0.0936	0.5162	-0.1746	0.9585	-23.8331	36.5439	-31.1991
2	4.4306	-0.7282	-0.3416	5.7028	2.5341	5.3523	0.1323	-0.2162	-0.1982	0.839	-0.1026	-0.3587	-0.0215	0.1697	-0.0297	0.196	-0.0211	0.0153	0.101	-0.0092	0.8897	-8.8531	33.3671	-12.8688
3	7.0552	-1.403	5.0748	1.3617	-1.5261	4.8356	-0.2221	0.4651	0.133	0.2339	0.08	-0.1546	-0.7031	0.2961	0.1421	0.8429	0.1773	0.3124	0.499	-0.2084	0.9313	-14.2356	59.1101	-21.2273
4	2.257	0.127	0.4187	1.2878	-0.5874	2.7145	-0.5729	0.8721	0.7233	0.2351	0.153	-0.1552	-1.0038	0.3859	0.4198	0.9819	-0.2274	0.3072	0.5546	0.0042	1.6646	-12.9875	59.043	-20.0549
5	3.1677	0.1506	1.0429	3.7996	2.9581	2.5744	-0.2161	-0.8357	-0.2913	0.1407	-0.1829	0.6063	0.0451	-0.3837	0.399	0.5294	0.3456	0.2336	0.3993	0.1089	1.3551	-31.6352	31.3344	2.6821
6	5.7684	0.4686	-1.4938	1.45	1.5281	4.1284	-0.2812	0.6198	-0.0259	-0.3848	0.4371	-0.243	-0.2405	-0.0643	-0.1559	0.4091	0.0784	0.1047	0.6449	0.0507	0.8737	-2.0835	30.6462	-46.496
7	2.8766	1.8169	0.8284	2.5774	0.0359	5.4104	-0.2313	-0.3245	-0.1684	0.488	0.0419	-0.1126	0.5341	0.3288	0.1894	0.5091	0.2463	0.1095	0.1639	-0.0721	0.8752	-47.2132	58.4844	25.0746
8	6.2262	-0.1971	-0.3949	3.1645	0.2755	3.9268	0.1184	0.4452	0.1813	-0.4176	-0.0832	0.1211	-0.4624	-0.0485	-0.0352	0.1688	0.0476	0.0923	0.0488	0.007	0.859	-49.7592	73.9612	7.2797
9	0.6342	-1.0873	-0.2781	5.627	-3.8743	5.2756	0.0746	-0.4512	0.0819	-0.3396	0.303	0.1076	0.4018	0.5014	-0.3777	0.6288	-0.1472	-0.15	1.0822	-0.2513	1.3798	-24.7549	68.8575	16.227
10	0.2426	0.2858	0.02	5.1429	-3.3626	4.5299	0.3054	-0.0511	-0.1695	-0.4212	-0.0637	0.2255	0.3115	0.7439	-0.2417	0.7444	0.0429	0.0268	1.0508	-0.3557	1.4225	-24.7516	70.0261	15.3481
11	5.3831	-0.0107	-2.3303	4.8788	0.9454	2.4819	0.2849	0.4164	-0.4145	-0.797	-0.2187	0.419	-0.208	-0.4357	-0.0661	0.294	0.1725	-0.0613	0.4003	-0.3844	1.0211	-50.7019	51.1819	-7.9552

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	D	7 - 222
2	X-RAY DIFFRACTION	2	F	6 - 222
3	X-RAY DIFFRACTION	3	G	2 - 31
4	X-RAY DIFFRACTION	4	I	2 - 31
5	X-RAY DIFFRACTION	5	J	4 - 88
6	X-RAY DIFFRACTION	6	H	4 - 89
7	X-RAY DIFFRACTION	7	A	7 - 222
8	X-RAY DIFFRACTION	8	B	6 - 222
9	X-RAY DIFFRACTION	9	C	4 - 31
10	X-RAY DIFFRACTION	10	E	2 - 31
11	X-RAY DIFFRACTION	11	K	4 - 88

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