PDB-2xul: Structure of PII from Synechococcus elongatus in complex with 2- ...

ID or keywords:

Entry

Database: PDB / ID: 2xul

Title

Structure of PII from Synechococcus elongatus in complex with 2- oxoglutarate at high 2-OG concentrations

Components

NITROGEN REGULATORY PROTEIN P-II

Keywords

SIGNALING PROTEIN / GLNK

Function / homology

Function and homology information

regulation of nitrogen utilization / enzyme regulator activity /

nucleotide binding / identical protein binding
Similarity search - Function

Biological species

SYNECHOCOCCUS ELONGATUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Zeth, K. / Chellamuthu, V.-R. / Forchhammer, K. / Fokina, O.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Mechanism of 2-Oxoglutarate Signaling by the Synechococcus Elongatus Pii Signal Transduction Protein
Authors: Fokina, O. / Chellamuthu, V.-R. / Forchhammer, K. / Zeth, K.

History

Deposition	Oct 19, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 3, 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

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2xul.cif.gz	257.8 KB	Display	PDBx/mmCIF format
PDB format	pdb2xul.ent.gz	222.5 KB	Display	PDB format
PDBx/mmJSON format	2xul.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/xu/2xul ftp://data.pdbj.org/pub/pdb/validation_reports/xu/2xul	HTTPS FTP

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Related structure data

Related structure data	2xzwC 1qy7 2jj4 2v5h 2xbp 2xg8 C: citing same article (ref.)
Similar structure data	3mct-d 1b42-d 1eqa-d 2xzw-2 4mpq-d 4dcg-d 4gvg-1 1jtf-d 1naq-1 6evu-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) 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	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1)

Deposited unit

A: NITROGEN REGULATORY PROTEIN P-II

B: NITROGEN REGULATORY PROTEIN P-II

C: NITROGEN REGULATORY PROTEIN P-II

D: NITROGEN REGULATORY PROTEIN P-II

E: NITROGEN REGULATORY PROTEIN P-II

F: NITROGEN REGULATORY PROTEIN P-II

hetero molecules

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

1

A: NITROGEN REGULATORY PROTEIN P-II

B: NITROGEN REGULATORY PROTEIN P-II

C: NITROGEN REGULATORY PROTEIN P-II

hetero molecules

defined by author&software
40.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: NITROGEN REGULATORY PROTEIN P-II

E: NITROGEN REGULATORY PROTEIN P-II

F: NITROGEN REGULATORY PROTEIN P-II

hetero molecules

defined by author&software
40.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	71.870, 87.987, 116.341
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
3	1	C
4	1	D
5	1	E
6	1	F

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	4	A	3 - 110
2	1	1	4	B	3 - 110
3	1	1	4	C	3 - 110
4	1	1	4	D	3 - 110
5	1	1	4	E	3 - 110
6	1	1	4	F	3 - 110

#1: Protein	NITROGEN REGULATORY PROTEIN P-II / PII SIGNAL TRANSDUCING PROTEIN / PII Mass: 12753.712 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: WITH C-TERMINAL STREP TAG / Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PASK-IBA3 (IBA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3F4
#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#3: Chemical	ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₅H₆O₅
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.4 Å³/Da / Density % sol: 48.78 % / Description: NONE
Crystal grow	pH: 7.4 / Details: pH 7.4

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Data collection

Diffraction	Mean temperature: 90 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→29 Å / Num. obs: 36239 / % possible obs: 99.6 % / Observed criterion σ(I): 2.6 / Redundancy: 7.2 % / R_merge(I) obs: 0.12 / Net I/σ(I): 2.6
Reflection shell	Resolution: 2.2→2.25 Å / Redundancy: 7.1 % / R_merge(I) obs: 0.78 / Mean I/σ(I) obs: 2.6 / % possible all: 98.1

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0102	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→29.09 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.933 / SU B: 9.663 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22488	1908	5 %	RANDOM
R_work	0.17929	-	-	-
obs	0.18161	36239	100 %	-

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: 27.941 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.95 Å²	0 Å²	0 Å²
2-	-	0.5 Å²	0 Å²
3-	-	-	0.45 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→29.09 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4918	0	252	247	5417

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.029	0.022	5207
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.041	2.029	7029
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.542	5	636
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.764	25	200
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.535	15	976
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.678	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.135	0.2	842
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	3646
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	0.865	1.5	3178
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.646	2	5139
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.113	3	2029
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.148	4.5	1889
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 / Number: 756 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	medium positional	0.34	0.5
2	B	medium positional	0.49	0.5
3	C	medium positional	0.39	0.5
4	D	medium positional	0.33	0.5
5	E	medium positional	0.42	0.5
6	F	medium positional	0.38	0.5
1	A	medium thermal	1.25	2
2	B	medium thermal	1.42	2
3	C	medium thermal	1.34	2
4	D	medium thermal	1.4	2
5	E	medium thermal	1.4	2
6	F	medium thermal	1.16	2

LS refinement shell

Resolution: 2.197→2.254 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	133	-
R_work	0.221	2522	-
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	0.5303	-0.2245	0.3705	1.7293	-0.2466	0.793	-0.0484	-0.1727	-0.0147	0.1399	0.0198	0.0675	-0.0401	-0.1696	0.0285	0.0282	0.0133	0.0041	0.077	-0.0067	0.0082	0.8777	-18.4718	20.9731
2	0.7695	-0.4807	0.2268	0.8016	-0.3621	0.79	-0.0495	-0.1295	0.0343	0.1275	0.032	-0.0317	-0.0358	-0.0771	0.0175	0.0291	0.0078	-0.0105	0.0539	-0.0134	0.0095	5.5636	-17.8763	20.2134
3	19.8272	3.0701	1.7907	17.1668	-9.0649	7.5786	0.1265	-0.4499	0.3623	0.4803	-0.1584	0.2322	-0.9855	0.2063	0.0318	0.2661	-0.0597	-0.0465	0.0644	-0.073	0.1549	4.8254	-0.0143	10.576
4	1.3463	0.7119	0.8766	0.3855	0.3696	2.189	-0.071	0.0371	-0.1058	-0.0445	0.0125	-0.0724	0.0983	0.0442	0.0584	0.019	0.0092	0.0092	0.0371	-0.016	0.0593	12.5838	-31.9572	7.6816
5	1.0965	-0.222	0.2363	0.7864	-0.3369	1.3354	0.0193	0.0326	-0.1471	-0.0723	0.002	0.0115	0.1267	-0.0833	-0.0213	0.0149	-0.0078	0.0007	0.0109	-0.0104	0.0299	12.4884	-30.2548	4.4897
6	0.5976	0.2186	0.2403	0.7856	0.381	1.3643	-0.0445	-0.0341	0.0048	0.0431	0.05	-0.1017	-0.1338	0.0372	-0.0056	0.0268	0.0105	-0.0121	0.0337	-0.002	0.0191	15.4064	-24.703	17.2845
7	0.5163	-0.2425	0.1535	0.6429	0.1035	0.8237	0.0012	0.0621	0.0074	-0.0265	-0.0434	-0.0112	0.0104	-0.0602	0.0422	0.0102	0.0153	-0.0051	0.0518	-0.0077	0.022	0.8536	-14.8967	0.1214
8	0.6682	-0.3614	0.0493	0.6825	0.1302	0.214	-0.0159	0.0601	0.0785	-0.0352	-0.0325	-0.0416	-0.0811	-0.0381	0.0484	0.0321	0.0097	-0.019	0.0636	-0.0044	0.02	4.5375	-13.1888	2.9679
9	8.569	-9.6221	11.8857	14.5729	-23.9787	46.528	0.0341	0.5846	0.3818	0.3328	0.1341	-0.1577	-0.9789	-1.1582	-0.1682	0.2124	-0.1341	0.0376	0.3762	0.0409	0.2654	20.7264	-20.6655	-4.7637
10	1.6131	0.1506	-0.3672	0.0397	0.1439	1.3637	-0.0757	-0.0144	-0.0276	-0.0297	-0.0062	0.0015	-0.1407	-0.034	0.0819	0.0638	-0.0052	-0.001	0.0108	0.0133	0.0479	26.2852	34.6726	7.6444
11	0.8685	-0.354	0.4417	0.6975	0.0042	0.6025	0.0203	0.029	0.0385	-0.0159	-0.0176	-0.058	-0.0928	0.0652	-0.0027	0.0325	-0.0166	0.0033	0.0279	0.0239	0.0356	26.9132	30.0898	4.2261
12	0.8035	-0.1894	0.6371	0.3359	-0.1775	0.5799	-0.0415	-0.1587	0.0019	0.0288	0.0495	0.0633	0.0278	-0.0913	-0.008	0.0648	0.0209	0.0067	0.0816	0.0106	0.0245	24.2916	26.4667	15.9832
13	0.676	-0.3244	0.1238	0.2312	-0.0375	0.2553	0.0082	0.0475	-0.029	-0.0183	-0.0335	0.0516	0.0889	-0.0247	0.0252	0.0446	-0.0221	-0.0021	0.0446	0.0025	0.0316	40.1914	14.2956	4.684
14	1.179	-0.5029	0.4021	0.2829	-0.0844	0.2496	0.0466	0.0496	-0.2048	0.0171	-0.0077	0.1113	0.056	0.0371	-0.0389	0.0568	-0.0275	-0.0051	0.0464	0.0129	0.0574	31.0439	13.5962	1.4356
15	13.3147	-8.7038	-3.6861	5.8231	4.8155	45.2016	0.6993	1.8188	-1.1296	-0.3084	-1.1349	0.7354	2.5224	-0.2143	0.4356	0.3761	-0.0137	-0.0563	0.376	-0.071	0.2516	18.5175	19.9911	-3.857
16	0.7371	-0.1144	0.3445	1.2874	-0.6878	1.0469	-0.1287	-0.1187	0.0733	0.0957	0.0786	-0.0485	-0.0673	0.0608	0.0501	0.0558	0.0031	-0.0218	0.0932	-0.0025	0.0177	36.979	25.8855	21.7338
17	0.6278	-0.3358	-0.0923	0.466	0.2256	0.735	-0.0258	-0.1579	-0.0908	0.0495	0.0481	0.0274	0.0518	-0.0354	-0.0223	0.0555	-0.0163	0.0004	0.0611	0.0381	0.0299	34.1956	18.4054	20.9082
18	4.3385	-2.9762	7.1106	7.7815	-5.1247	11.7435	0.2736	-0.1468	-0.2573	0.452	0.0318	0.718	0.5695	-0.2101	-0.3053	0.2814	0.0066	0.2237	0.0227	0.0832	0.4627	35.6411	1.2285	12.4494

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 38
2	X-RAY DIFFRACTION	2	A	39 - 106
3	X-RAY DIFFRACTION	3	A	107 - 113
4	X-RAY DIFFRACTION	4	B	1 - 16
5	X-RAY DIFFRACTION	5	B	17 - 82
6	X-RAY DIFFRACTION	6	B	83 - 113
7	X-RAY DIFFRACTION	7	C	1 - 39
8	X-RAY DIFFRACTION	8	C	40 - 107
9	X-RAY DIFFRACTION	9	C	108 - 113
10	X-RAY DIFFRACTION	10	D	1 - 21
11	X-RAY DIFFRACTION	11	D	22 - 82
12	X-RAY DIFFRACTION	12	D	83 - 113
13	X-RAY DIFFRACTION	13	E	1 - 69
14	X-RAY DIFFRACTION	14	E	70 - 103
15	X-RAY DIFFRACTION	15	E	104 - 109
16	X-RAY DIFFRACTION	16	F	1 - 53
17	X-RAY DIFFRACTION	17	F	54 - 104
18	X-RAY DIFFRACTION	18	F	105 - 113

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