PDB-2xhk: Crystal structure of transcription factor NtcA from Synechococcus...

ID or keywords:

Entry

Database: PDB / ID: 2xhk

Title

Crystal structure of transcription factor NtcA from Synechococcus elongatus bound to 2-oxoglutarate

Components

GLOBAL NITROGEN REGULATOR

Keywords

TRANSCRIPTION /

NITROGEN ASSIMILATION / CRP/FNR SUPERFAMILY /

2-OXOGLUTARATE / GLOBAL NITROGEN CONTROLLER.

Function / homology

Function and homology information

DNA-binding transcription factor activity /

Biological species

SYNECHOCOCCUS ELONGATUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Llacer, J.L. / Castells, M.A. / Rubio, V.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural Basis for the Regulation of Ntca-Dependent Transcription by Proteins Pipx and Pii.
Authors: Llacer, J.L. / Espinosa, J. / Castells, M.A. / Contreras, A. / Forchhammer, K. / Rubio, V.

History

Deposition	Jun 17, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 18, 2010	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xh/2xhk ftp://data.pdbj.org/pub/pdb/validation_reports/xh/2xhk	HTTPS FTP

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Related structure data

Related structure data	2xg8C 2xgxSC 2xkoC 2xkpC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6anv-2 2xgx-d 2xkp-1 2xkp-2 4rui-4 5cvr-1 3hgk-4 6anv-1 3mdr-1 3qcz-d 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
Related items in Molecule of the Month	#48 - Dec 2003 Catabolite Activator Protein similarity (11) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (5) #251 - Nov 2020 Adenylyl Cyclase similarity (5) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1)

Deposited unit

A: GLOBAL NITROGEN REGULATOR

B: GLOBAL NITROGEN REGULATOR

hetero molecules

50 kDa, 2 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)	68.220, 70.810, 149.960
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	LEU	LEU	3	A	A	8 - 20	8 - 20
2	1	LEU	LEU	LEU	LEU	3	B	B	8 - 20	8 - 20
1	2	PRO	PRO	GLY	GLY	2	A	A	21 - 30	21 - 30
2	2	PRO	PRO	GLY	GLY	2	B	B	21 - 30	21 - 30
1	3	GLU	GLU	GLU	GLU	2	A	A	61	61
2	3	GLU	GLU	GLU	GLU	2	B	B	61	61
1	4	GLU	GLU	LEU	LEU	1	A	A	62 - 80	62 - 80
2	4	GLU	GLU	LEU	LEU	1	B	B	62 - 80	62 - 80
1	5	SER	SER	SER	SER	6	A	A	222	222
2	5	SER	SER	SER	SER	6	B	B	222	222
1	6	SER	SER	ILE	ILE	1	A	A	85 - 104	85 - 104
2	6	SER	SER	ILE	ILE	1	B	B	85 - 104	85 - 104
1	7	GLU	GLU	GLU	GLU	3	A	A	105	105
2	7	GLU	GLU	GLU	GLU	3	B	B	105	105
1	8	MET	MET	ILE	ILE	1	A	A	107 - 112	107 - 112
2	8	MET	MET	ILE	ILE	1	B	B	107 - 112	107 - 112
1	9	PRO	PRO	LEU	LEU	4	A	A	115 - 117	115 - 117
2	9	PRO	PRO	LEU	LEU	4	B	B	115 - 117	115 - 117
1	10	ALA	ALA	SER	SER	1	A	A	118 - 127	118 - 127
2	10	ALA	ALA	SER	SER	1	B	B	118 - 127	118 - 127
1	11	ARG	ARG	ARG	ARG	2	A	A	142	142
2	11	ARG	ARG	ARG	ARG	2	B	B	142	142
1	12	ASP	ASP	PRO	PRO	1	A	A	143 - 162	143 - 162
2	12	ASP	ASP	PRO	PRO	1	B	B	143 - 162	143 - 162
1	13	ARG	ARG	ARG	ARG	3	A	A	186	186
2	13	ARG	ARG	ARG	ARG	3	B	B	186	186
1	14	VAL	VAL	THR	THR	1	A	A	187 - 190	187 - 190
2	14	VAL	VAL	THR	THR	1	B	B	187 - 190	187 - 190
1	15	ARG	ARG	ARG	ARG	3	A	A	191	191
2	15	ARG	ARG	ARG	ARG	3	B	B	191	191
1	16	LEU	LEU	ARG	ARG	1	A	A	192 - 197	192 - 197
2	16	LEU	LEU	ARG	ARG	1	B	B	192 - 197	192 - 197
1	17	PHE	PHE	PHE	PHE	1	A	A	221	221
2	17	PHE	PHE	PHE	PHE	1	B	B	221	221
1	18	SER	SER	ILE	ILE	1	A	A	199 - 204	199 - 204
2	18	SER	SER	ILE	ILE	1	B	B	199 - 204	199 - 204
1	19	LYS	LYS	ARG	ARG	3	A	A	206 - 208	206 - 208
2	19	LYS	LYS	ARG	ARG	3	B	B	206 - 208	206 - 208
1	20	ILE	ILE	SER	SER	1	A	A	209 - 218	209 - 218
2	20	ILE	ILE	SER	SER	1	B	B	209 - 218	209 - 218
1	21	SER	SER	ASP	ASP	5	A	A	163 - 165	163 - 165
2	21	SER	SER	ASP	ASP	5	B	B	163 - 165	163 - 165
1	22	GLY	GLY	LEU	LEU	1	A	A	166 - 171	166 - 171
2	22	GLY	GLY	LEU	LEU	1	B	B	166 - 171	166 - 171
1	23	LYS	LYS	LYS	LYS	2	A	A	31	31
2	23	LYS	LYS	LYS	LYS	2	B	B	31	31
1	24	THR	THR	ALA	ALA	1	A	A	32 - 40	32 - 40
2	24	THR	THR	ALA	ALA	1	B	B	32 - 40	32 - 40
1	25	GLU	GLU	GLU	GLU	5	A	A	41	41
2	25	GLU	GLU	GLU	GLU	5	B	B	41	41
1	26	ARG	ARG	TYR	TYR	1	A	A	42 - 57	42 - 57
2	26	ARG	ARG	TYR	TYR	1	B	B	42 - 57	42 - 57
1	27	GLU	GLU	SER	SER	5	A	A	58 - 59	58 - 59
2	27	GLU	GLU	SER	SER	5	B	B	58 - 59	58 - 59
1	28	GLY	GLY	GLY	GLY	1	A	A	60	60
2	28	GLY	GLY	GLY	GLY	1	B	B	60	60
1	29	LYS	LYS	LYS	LYS	2	A	A	172	172
2	29	LYS	LYS	LYS	LYS	2	B	B	172	172
1	30	LEU	LEU	THR	THR	1	A	A	173 - 185	173 - 185
2	30	LEU	LEU	THR	THR	1	B	B	173 - 185	173 - 185
1	31	GLN	GLN	GLN	GLN	4	A	A	219 - 220	219 - 220
2	31	GLN	GLN	GLN	GLN	4	B	B	219 - 220	219 - 220
1	32	ARG	ARG	ARG	ARG	3	A	A	128	128
2	32	ARG	ARG	ARG	ARG	3	B	B	128	128
1	33	ILE	ILE	HIS	HIS	1	A	A	129 - 141	129 - 141
2	33	ILE	ILE	HIS	HIS	1	B	B	129 - 141	129 - 141

NCS oper: (Code: given
Matrix: (-0.3962, -0.9012, -0.1755), (-0.9044, 0.35, 0.2441), (-0.1586, 0.2554, -0.9537)
Vector: 19.7872, 20.7884, -40.4147)

#1: Protein	GLOBAL NITROGEN REGULATOR / NTCA Mass: 24862.053 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA / References: UniProt: P29283
#2: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₆O₅
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.35 Å³/Da / Density % sol: 63.35 % / Description: NONE
Crystal grow	pH: 5.5 Details: NTCA PROTEIN WAS AT 4.7 MG/ML IN 50 MM SODIUM CITRATE PH 6.5, 0.5 M NACL, 5 MM MAGNESIUM CHLORIDE, 50 MM ARGININE HYDROCHLORIDE, 50 MM NA L-GLUTAMATE, 10 MM 2-OXOGLUTARATE (2OG). ...Details: NTCA PROTEIN WAS AT 4.7 MG/ML IN 50 MM SODIUM CITRATE PH 6.5, 0.5 M NACL, 5 MM MAGNESIUM CHLORIDE, 50 MM ARGININE HYDROCHLORIDE, 50 MM NA L-GLUTAMATE, 10 MM 2-OXOGLUTARATE (2OG). CRYSTALLIZATION SOLUTION: 0.1 M BIS-TRIS PH 5.5, 11 % PEG 10000, 0.15 M AMMONIUM ACETATE

Crystal

Density Matthews: 3.35 Å³/Da / Density % sol: 63.35 % / Description: NONE

Crystal grow

pH: 5.5
Details: NTCA PROTEIN WAS AT 4.7 MG/ML IN 50 MM SODIUM CITRATE PH 6.5, 0.5 M NACL, 5 MM MAGNESIUM CHLORIDE, 50 MM ARGININE HYDROCHLORIDE, 50 MM NA L-GLUTAMATE, 10 MM 2-OXOGLUTARATE (2OG). ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
Detector	Type: ADSC CCD / Detector: CCD / Date: Jun 27, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.3→75 Å / Num. obs: 32971 / % possible obs: 99.8 % / Observed criterion σ(I): 1.8 / Redundancy: 7.1 % / B_iso Wilson estimate: 47.6 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 13.3
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.44 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0072	refinement
XDS		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XGX

2xgx

Resolution: 2.3→50 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.932 / SU B: 11.287 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23769	1673	5.1 %	RANDOM
R_work	0.20393	-	-	-
obs	0.20566	31296	99.77 %	-

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: 47.081 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.48 Å²	0 Å²	0 Å²
2-	-	1.04 Å²	0 Å²
3-	-	-	-1.53 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3396	0	20	116	3532

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	3489
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2439
X-RAY DIFFRACTION	r_angle_refined_deg	1.563	1.99	4709
X-RAY DIFFRACTION	r_angle_other_deg	0.953	3	5926
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.542	5	434
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.823	22.74	146
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.307	15	646
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.042	15	33
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	558
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3790
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	715
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	0.684	1.5	2157
X-RAY DIFFRACTION	r_mcbond_other	0.157	1.5	873
X-RAY DIFFRACTION	r_mcangle_it	1.251	2	3496
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.019	3	1332
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.234	4.5	1210
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

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	2230	tight positional	0.27	0.05
2	B	2230	tight positional	0.27	0.05
1	A	253	medium positional	0.63	0.5
2	B	253	medium positional	0.63	0.5
1	A	216	loose positional	0.77	5
2	B	216	loose positional	0.77	5
1	A	2230	tight thermal	1.11	0.5
2	B	2230	tight thermal	1.11	0.5
1	A	253	medium thermal	1.38	2
2	B	253	medium thermal	1.38	2
1	A	216	loose thermal	1.4	10
2	B	216	loose thermal	1.4	10

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.329	112	-
R_work	0.278	2307	-
obs	-	-	99.96 %

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	11.0499	-7.2945	-1.4524	6.4289	-2.4465	7.7044	-0.1025	0.2333	0.48	0.4802	0.2912	-0.0087	-0.9607	-1.1241	-0.1888	0.5102	0.0763	-0.1456	0.4667	-0.0889	0.9334	-17.953	41.837	-30.566
2	2.8583	0.2402	0.1836	3.7172	-0.3288	4.1298	-0.005	0.1674	0.0047	-0.2299	0.024	0.0311	-0.2496	0.0378	-0.0189	0.1831	0.028	-0.0246	0.0951	0.0509	0.07	-1.944	32.734	-30.644
3	4.1158	-0.936	0.269	2.1124	0.1012	5.1203	0.016	-0.2746	0.8487	0.2041	0.0222	0.091	-1.0699	-0.364	-0.0383	0.4168	0.0713	0.0193	0.2074	0.046	0.2928	-6.922	42.016	-26.03
4	1.0077	0.6722	0.1069	3.5089	0.2963	3.7316	0.0221	-0.0332	-0.031	-0.0367	-0.0197	0.1364	0.0967	-0.0975	-0.0025	0.0762	-0.0117	-0.0148	0.1301	-0.0032	0.0309	-5.536	21.289	-18.904
5	4.0618	-1.3835	0.4336	4.5874	1.0995	2.8076	0.1178	0.2076	-0.3102	-0.2637	-0.0377	0.4872	0.3486	-0.2425	-0.0801	0.2469	-0.0183	-0.0788	0.1247	0.0059	0.0782	-6.085	10.891	-31.458
6	4.8433	-1.3753	-0.1291	2.9619	1.7742	11.0446	0.131	-0.8388	-0.3501	0.4623	-0.1502	0.239	0.1677	0.016	0.0193	0.2979	-0.0984	-0.0864	0.3013	0.0145	0.3498	-11.802	8.812	-23.768
7	1.3611	-0.604	-0.2391	8.6901	-3.1002	13.7085	-0.0449	-0.4805	1.0161	0.6913	-0.1827	0.1312	-2.0357	-0.4279	0.2277	0.5215	0.0579	-0.053	0.4832	-0.296	0.8947	-4.77	43.88	1.222
8	4.0385	0.7402	-0.7156	4.0442	-0.141	3.3744	0.036	-0.2042	0.081	0.1055	0.0233	0.2118	-0.2425	-0.2227	-0.0593	0.0585	0.0206	0.0147	0.1616	0.002	0.0178	-5.27	26.3	-3.222
9	2.5785	-0.0117	0.5857	4.1578	0.6282	3.4866	-0.0121	-0.2621	0.5943	0.0546	-0.0678	0.6427	-1.0072	-0.4878	0.08	0.3286	0.0956	0.0435	0.2746	-0.0673	0.2686	-8.565	38.792	-4.139
10	4.3776	-1.1082	1.5512	1.6476	-0.8615	2.8264	0.0383	0.1564	-0.0827	-0.1765	0.0109	-0.0626	0.0308	0.168	-0.0491	0.0746	-0.0211	-0.0072	0.1236	0.0308	0.06	8.021	26.172	-16.503
11	4.3425	-1.3702	0.447	4.0389	0.0599	3.101	0.0089	-0.0911	0.2176	0.1503	0.0689	-0.3726	-0.1734	0.3816	-0.0777	0.047	-0.01	-0.0164	0.2075	0.0056	0.053	18.146	22.444	-6.154
12	10.9037	6.1603	12.9911	5.7159	3.7621	21.212	-0.3114	0.3896	-0.0065	-0.2854	0.4131	0.0647	-0.2343	0.1156	-0.1018	0.3114	-0.021	0.066	0.4681	-0.0039	0.3822	20.278	29.535	-20.355

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 26
2	X-RAY DIFFRACTION	2	A	27 - 79
3	X-RAY DIFFRACTION	3	A	80 - 118
4	X-RAY DIFFRACTION	4	A	119 - 156
5	X-RAY DIFFRACTION	5	A	157 - 206
6	X-RAY DIFFRACTION	6	A	207 - 222
7	X-RAY DIFFRACTION	7	B	4 - 26
8	X-RAY DIFFRACTION	8	B	27 - 88
9	X-RAY DIFFRACTION	9	B	89 - 123
10	X-RAY DIFFRACTION	10	B	124 - 156
11	X-RAY DIFFRACTION	11	B	157 - 213
12	X-RAY DIFFRACTION	12	B	214 - 222

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