PDB-2xkp: NtcA from Synechococcus elongatus: active and inactive

ID or keywords:

Entry

Database: PDB / ID: 2xkp

Title

NtcA from Synechococcus elongatus: active and inactive

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: 3.05 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	Jul 11, 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_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_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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Download

PDBx/mmCIF format	2xkp.cif.gz	245.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2xkp.ent.gz	199.2 KB	Display	PDB format
PDBx/mmJSON format	2xkp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	2xg8C 2xgxC 2xhkSC 2xkoC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2xgx-d 1vjt-d 6anv-2 2xhk-d 5yez-1 7br4-d 5ydo-1 4rui-4 6kcx-d 1z3z-d Search similar-shape structures by Omokage search (details) 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

Related structure data

2xg8C

2xgxC

2xhkSC

2xkoC

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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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

C: GLOBAL NITROGEN REGULATOR

D: GLOBAL NITROGEN REGULATOR

E: GLOBAL NITROGEN REGULATOR

F: GLOBAL NITROGEN REGULATOR

hetero molecules

150 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GLOBAL NITROGEN REGULATOR

B: GLOBAL NITROGEN REGULATOR

hetero molecules

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

2

D: GLOBAL NITROGEN REGULATOR

E: GLOBAL NITROGEN REGULATOR

hetero molecules

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

3

C: GLOBAL NITROGEN REGULATOR

F: GLOBAL NITROGEN REGULATOR

hetero molecules

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

Unit cell

Length a, b, c (Å)	110.391, 110.391, 219.600
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	D
4	1	E
1	2	C
2	2	F
1	3	A
2	3	D
1	4	B
2	4	E

NCS domain segments:
NCS ensembles :

ID
1
2
3
4

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.9965, 0.084, -0.005), (-0.0356, -0.3671, 0.9295), (0.0762, 0.9264, 0.3688)	-56.833, -34.451, 24.7838
2	given	(-0.5004, 0.8658, 0.0005), (0.8658, 0.5004, -0.0002), (-0.0004, 0.0003, -1)	-0.0101, 0.0075, -58.1793
3	given	(-0.9965, -0.0839, -0.005), (0.0355, -0.367, -0.9295), (0.0762, -0.9264, 0.3687)	-163.6549, -50.6106, -30.0116
4	given	(-1, -0.0001), (-0.0001, 1), (-1)	-110.3885, -0.0048, -21.6276
5	given	(-0.37942, 0.25251, -0.8901), (-0.92509, -0.12012, 0.36026), (-0.01595, 0.96011, 0.27917)	-104.4732, -52.2381, 42.1877
6	given	(0.37952, -0.25251, 0.89006), (-0.92505, -0.12013, 0.36036), (0.01593, -0.96011, -0.27918)	-5.9089, -52.2277, -63.8192

#1: Protein	GLOBAL NITROGEN REGULATOR / NTCA Mass: 24862.053 Da / Num. of mol.: 6 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.: 6 / Source method: obtained synthetically / Formula: C₅H₆O₅

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.45 % / Description: NONE
Crystal grow	pH: 8.3 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. CRYSTALLIZATION ...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. CRYSTALLIZATION SOLUTION: 0.2 M POTASSIUM CITRATE PH 8.3, 20 % PEG-3350.

Crystal

Density Matthews: 2.38 Å³/Da / Density % sol: 48.45 % / Description: NONE

Crystal grow

pH: 8.3
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. CRYSTALLIZATION ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.984
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 26, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.984 Å / Relative weight: 1
Reflection	Resolution: 3.05→87.7 Å / Num. obs: 28882 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 11.2 % / B_iso Wilson estimate: 69.1 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 5.6
Reflection shell	Resolution: 3.05→3.21 Å / Redundancy: 11.4 % / R_merge(I) obs: 0.43 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XHK

2xhk

Resolution: 3.05→50 Å / Cor.coef. F_o:F_c: 0.926 / Cor.coef. F_o:F_c free: 0.889 / SU B: 39.224 / SU ML: 0.322 / Cross valid method: THROUGHOUT / ESU R Free: 0.454 / 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	0.2474	1461	5.1 %	RANDOM
R_work	0.20621	-	-	-
obs	0.20828	27354	99.98 %	-

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: 54.478 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.78 Å²	0.39 Å²	0 Å²
2-	-	0.78 Å²	0 Å²
3-	-	-	-1.17 Å²

Refinement step

Cycle: LAST / Resolution: 3.05→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9506	0	60	0	9566

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	9710
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	6654
X-RAY DIFFRACTION	r_angle_refined_deg	1.222	1.989	13120
X-RAY DIFFRACTION	r_angle_other_deg	0.892	3	16184
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.295	5	1212
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.756	22.684	380
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	21.719	15	1724
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.487	15	82
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1588
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	10532
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1970
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	0.385	1.5	6108
X-RAY DIFFRACTION	r_mcbond_other	0.047	1.5	2472
X-RAY DIFFRACTION	r_mcangle_it	0.746	2	9862
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.033	3	3602
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.937	4.5	3258
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

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1084	tight positional	0.04	0.05
1	2	B	1084	tight positional	0.04	0.05
1	1	C	1084	tight positional	0.04	0.05
1	3	D	1084	tight positional	0.04	0.05
2	1	C	2565	tight positional	0.01	0.05
2	2	F	2565	tight positional	0.01	0.05
3	1	A	2741	tight positional	0	0.05
3	2	D	2741	tight positional	0	0.05
4	1	B	2762	tight positional	0.01	0.05
4	2	E	2762	tight positional	0.01	0.05
1	1	A	349	medium positional	0.03	0.5
1	2	B	349	medium positional	0.03	0.5
1	1	C	349	medium positional	0.03	0.5
1	3	D	349	medium positional	0.03	0.5
1	1	A	106	loose positional	0.02	5
1	2	B	106	loose positional	0.02	5
1	1	C	106	loose positional	0.02	5
1	3	D	106	loose positional	0.02	5
1	1	A	1084	tight thermal	0.04	0.5
1	2	B	1084	tight thermal	0.04	0.5
1	1	C	1084	tight thermal	0.04	0.5
1	3	D	1084	tight thermal	0.04	0.5
2	1	C	2565	tight thermal	0.02	0.5
2	2	F	2565	tight thermal	0.02	0.5
3	1	A	2741	tight thermal	0.01	0.5
3	2	D	2741	tight thermal	0.01	0.5
4	1	B	2762	tight thermal	0.01	0.5
4	2	E	2762	tight thermal	0.01	0.5
1	1	A	349	medium thermal	0.04	2
1	2	B	349	medium thermal	0.04	2
1	1	C	349	medium thermal	0.04	2
1	3	D	349	medium thermal	0.04	2
1	1	A	106	loose thermal	0.04	10
1	2	B	106	loose thermal	0.04	10
1	1	C	106	loose thermal	0.04	10
1	3	D	106	loose thermal	0.04	10

LS refinement shell

Resolution: 3.05→3.129 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.305	103	-
R_work	0.267	2027	-
obs	-	-	100 %

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	1.476	1.5863	1.1637	4.1632	0.2781	3.3254	-0.0736	-0.0409	0.2816	0.193	0.0845	-0.0814	-0.6309	0.6571	-0.0109	0.3828	-0.1172	-0.0064	0.3617	-0.0611	0.3567	-24.433	-12.041	0.803
2	2.8436	-0.3623	2.1158	4.4047	-0.6553	4.0194	0.002	0.0893	0.1833	-0.1873	-0.0082	0.141	-0.2182	0.119	0.0063	0.1851	-0.0364	0.0007	0.1339	0.0337	0.1384	-38.514	-19.173	-18.264
3	2.8123	-0.0266	-0.7415	3.0922	-0.8773	3.2316	0.1619	-0.3046	0.2969	0.3745	-0.0264	0.1742	-0.4061	0.0632	-0.1354	0.1265	-0.0138	-0.0257	0.1207	-0.0171	0.1777	-33.891	-28.782	10.241
4	4.3092	-0.0276	3.7573	2.5519	0.531	5.934	0.2288	0.1617	-0.0576	-0.0091	-0.0785	-0.5174	0.678	0.5826	-0.1503	0.1455	0.1172	0.0125	0.1645	0	0.145	-22.31	-45.675	-0.429
5	5.2285	2.4121	1.1564	5.1672	0.8369	4.8455	0.2206	-0.5809	-0.7372	0.1142	-0.1901	0.0679	0.777	-0.5405	-0.0304	0.1544	-0.0327	-0.0222	0.2319	0.0542	0.1563	-41.584	-60.086	-16.878
6	3.5736	-2.0863	0.7942	2.7557	0.4509	2.2513	0.0107	0.0198	-0.1141	-0.0584	-0.1191	0.2674	0.1157	-0.2104	0.1084	0.05	0.0212	0.0004	0.1385	-0.0034	0.0368	-47.133	-43.167	-30.098
7	1.1258	-1.3942	0.9825	4.6585	-0.4118	3.2291	-0.0575	0.0291	0.2808	-0.2166	0.1014	0.0628	-0.6043	-0.6896	-0.044	0.36	0.1021	-0.0069	0.3717	0.0567	0.3667	-85.954	-12.044	-22.463
8	2.5239	0.2975	2.0952	4.5697	0.6902	3.1959	0.0296	-0.0497	0.1506	0.2151	0.0359	-0.1099	-0.2866	-0.1427	-0.0654	0.206	0.0161	0.0019	0.132	-0.0254	0.1354	-71.874	-19.178	-3.397
9	2.7148	0.069	-0.7687	3.151	0.8067	2.6744	0.1777	0.2959	0.3108	-0.3787	-0.0371	-0.1767	-0.3795	-0.0689	-0.1406	0.1327	0.0138	-0.0339	0.1356	0.0264	0.1842	-76.496	-28.792	-31.905
10	3.8578	0.4169	4.089	2.0107	-0.1168	5.4763	0.2726	-0.1761	-0.0215	0.0317	-0.1094	0.5473	0.7175	-0.5173	-0.1633	0.2122	-0.1427	0.0152	0.2066	-0.008	0.1616	-88.077	-45.683	-21.232
11	2.5779	0.1373	-2.8758	0.225	-0.1254	3.2255	-0.1053	0.6408	-0.0779	0.1528	0.0129	0.1508	0.1906	-0.6741	0.0924	0.3418	0.0812	-0.0024	0.3391	-0.0183	0.2407	-68.811	-60.088	-4.781
12	3.3458	-0.6264	-1.9179	0.4302	0.3104	1.3569	0.0495	-0.5052	0.3148	0.1694	0.145	0.1528	-0.0807	0.1063	-0.1945	0.2686	0.052	0.028	0.3161	0.0114	0.2499	-63.262	-43.168	8.437

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 141
2	X-RAY DIFFRACTION	2	A	142 - 222
3	X-RAY DIFFRACTION	3	B	6 - 156
4	X-RAY DIFFRACTION	4	B	157 - 220
5	X-RAY DIFFRACTION	5	C	21 - 119
6	X-RAY DIFFRACTION	6	C	120 - 219
7	X-RAY DIFFRACTION	7	D	5 - 141
8	X-RAY DIFFRACTION	8	D	142 - 222
9	X-RAY DIFFRACTION	9	E	6 - 156
10	X-RAY DIFFRACTION	10	E	157 - 220
11	X-RAY DIFFRACTION	11	F	21 - 119
12	X-RAY DIFFRACTION	12	F	120 - 219

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