PDB-2xg8: Structural basis of gene regulation by protein PII: The crystal c...

ID or keywords:

Entry

Database: PDB / ID: 2xg8

Title

Structural basis of gene regulation by protein PII: The crystal complex of PII and PipX from Synechococcus elongatus PCC 7942

Components

NITROGEN REGULATORY PROTEIN P-II
PIPX

Keywords

TRANSCRIPTION / PII SIGNALING PROTEIN / NTCA CO-ACTIVATOR PROTEIN PIPX / TUDOR-LIKE DOMAIN

Function / homology

Function and homology information

regulation of nitrogen utilization / enzyme regulator activity / ATP binding / identical protein binding / cytosol
Similarity search - Function

Biological species

SYNECHOCOCCUS ELONGATUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Llacer, J.L. / 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 1, 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 / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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	2xg8.cif.gz	244.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2xg8.ent.gz	199.8 KB	Display	PDB format
PDBx/mmJSON format	2xg8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2xg8_validation.pdf.gz	457.5 KB	Display	wwPDB validaton report
Full document	2xg8_full_validation.pdf.gz	471.7 KB	Display
Data in XML	2xg8_validation.xml.gz	22.3 KB	Display
Data in CIF	2xg8_validation.cif.gz	31.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/2xg8 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xg8	HTTPS FTP

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Related structure data

Related structure data	2xgxC 2xhkC 2xkoC 2xkpC 1v5hS 1qy7 2jj4 2v5h 2xbp C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3vqx-d 2wmi-d 2wmj-d 3omi-d 3oma-d 3fye-d 1l8p-d 6pw0-d 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

Deposited unit

A: NITROGEN REGULATORY PROTEIN P-II

B: NITROGEN REGULATORY PROTEIN P-II

C: NITROGEN REGULATORY PROTEIN P-II

D: PIPX

E: PIPX

F: PIPX

68.9 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

D: PIPX

E: PIPX

F: PIPX

A: NITROGEN REGULATORY PROTEIN P-II

B: NITROGEN REGULATORY PROTEIN P-II

C: NITROGEN REGULATORY PROTEIN P-II

D: PIPX

E: PIPX

F: PIPX

defined by author&software
138 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	111.383, 61.585, 112.979
Angle α, β, γ (deg.)	90.00, 126.44, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 36
2	1	1	1	B	1 - 36
3	1	1	1	C	1 - 36
1	2	1	1	A	48 - 100
2	2	1	1	B	48 - 100
3	2	1	1	C	48 - 100
1	3	1	4	A	37 - 43
2	3	1	4	B	37 - 43
3	3	1	4	C	37 - 43
1	4	1	3	A	44 - 47
2	4	1	3	B	44 - 47
3	4	1	3	C	44 - 47
1	5	1	3	A	101
2	5	1	3	B	101
3	5	1	3	C	101
1	6	1	1	A	102 - 105
2	6	1	1	B	102 - 105
3	6	1	1	C	102 - 105
1	7	1	3	A	106 - 108
2	7	1	3	B	106 - 108
3	7	1	3	C	106 - 108
1	1	2	4	A	109 - 112
2	1	2	4	C	109 - 112
1	1	3	1	D	1 - 7
2	1	3	1	E	1 - 7
3	1	3	1	F	1 - 7
1	2	3	2	D	8
2	2	3	2	E	8
3	2	3	2	F	8
1	3	3	1	D	9 - 19
2	3	3	1	E	9 - 19
3	3	3	1	F	9 - 19
1	4	3	2	D	59
2	4	3	2	E	59
3	4	3	2	F	59
1	5	3	1	D	60 - 62
2	5	3	1	E	60 - 62
3	5	3	1	F	60 - 62
1	6	3	1	D	49 - 58
2	6	3	1	E	49 - 58
3	6	3	1	F	49 - 58
1	7	3	4	D	42 - 47
2	7	3	4	E	42 - 47
3	7	3	4	F	42 - 47
1	8	3	2	D	34
2	8	3	2	E	34
3	8	3	2	F	34
1	9	3	1	D	35 - 41
2	9	3	1	E	35 - 41
3	9	3	1	F	35 - 41
1	10	3	4	D	20 - 25
2	10	3	4	E	20 - 25
3	10	3	4	F	20 - 25
1	11	3	1	D	26 - 33
2	11	3	1	E	26 - 33
3	11	3	1	F	26 - 33
1	12	3	2	D	63
2	12	3	2	E	63
3	12	3	2	F	63
1	13	3	1	D	64 - 65
2	13	3	1	E	64 - 65
3	13	3	1	F	64 - 65
1	14	3	2	D	66 - 67
2	14	3	2	E	66 - 67
3	14	3	2	F	66 - 67
1	15	3	4	D	68 - 70
2	15	3	4	E	68 - 70
3	15	3	4	F	68 - 70

NCS ensembles :

ID
1
2
3

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.4831, 0.6214, -0.6168), (-0.2832, 0.5558, 0.7816), (0.8285, 0.5522, -0.0925)	-0.6438, -18.4586, 29.623
2	given	(-0.461, -0.3084, 0.8321), (0.6209, 0.5579, 0.5507), (-0.634, 0.7705, -0.0657)	-29.9665, -5.8087, 16.3787
3	given	(-0.4795, 0.6309, -0.6099), (-0.2875, 0.5438, 0.7885), (0.8291, 0.5534, -0.0794)	-0.4542, -18.5293, 29.2755
4	given	(-0.4522, -0.2814, 0.8463), (0.66, 0.5326, 0.5298), (-0.5998, 0.7982, -0.0551)	-29.5687, -4.3909, 15.998
5	given	(-0.484, 0.6569, -0.5781), (-0.2541, 0.5267, 0.8112), (0.8374, 0.5395, -0.088)	-1.2812, -19.2277, 29.6092
6	given	(-0.4435, -0.2789, 0.8518), (0.6704, 0.5274, 0.5218), (-0.5948, 0.8025, -0.0469)	-30.7316, -4.91, 15.1005

#1: Protein	NITROGEN REGULATORY PROTEIN P-II / PII SIGNAL TRANSDUCING PROTEIN Mass: 12409.347 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET-22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3F4
#2: Protein	PIPX Mass: 10540.987 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7X386
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.19 Å³/Da / Density % sol: 43.82 % / Description: NONE
Crystal grow	pH: 7.5 Details: PII-PIPX COMPLEX AT 5.5 MG/ML IN 20 MM HEPES PH 7.5, 1MM DTT, 0.4 M NACL, 5 MM MAGNESIUM CHLORIDE. PRECIPITANT SOLUTION: 15 % PEG 3.35K, 0.2 M SODIUM FORMATE.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
Detector	Type: ADSC CCD / Detector: CCD / Date: Nov 10, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 3.2→90.9 Å / Num. obs: 10330 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Redundancy: 3.9 % / B_iso Wilson estimate: 74.4 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 7.1
Reflection shell	Resolution: 3→3.37 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V5H, CHAIN J

1v5h

Resolution: 3.2→50 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c free: 0.865 / SU B: 59.859 / SU ML: 0.476 / Cross valid method: THROUGHOUT / ESU R Free: 0.603 / 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	0.27247	495	4.8 %	RANDOM
R_work	0.22708	-	-	-
obs	0.22923	9829	99.83 %	-

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: 70.104 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.51 Å²	0 Å²	1.6 Å²
2-	-	0.05 Å²	0 Å²
3-	-	-	0.35 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4529	0	0	3	4532

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4596
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	3169
X-RAY DIFFRACTION	r_angle_refined_deg	1.259	1.959	6187
X-RAY DIFFRACTION	r_angle_other_deg	1.009	3	7668
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.25	5	571
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.799	23.514	222
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.696	15	812
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.408	15	43
X-RAY DIFFRACTION	r_chiral_restr	0.142	0.2	707
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	5128
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	995
X-RAY DIFFRACTION	r_nbd_refined	0.228	0.2	1037
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	3306
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	2213
X-RAY DIFFRACTION	r_nbtor_other	0.083	0.2	2711
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.122	0.2	124
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	0.244	0.2	39
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.236	0.2	77
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.3	0.2	3
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	0.337	1.5	3677
X-RAY DIFFRACTION	r_mcbond_other	0.031	1.5	1181
X-RAY DIFFRACTION	r_mcangle_it	0.375	2	4567
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.475	3	2001
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	0.763	4.5	1620
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	1246	tight positional	0.02	0.05
1	2	B	1246	tight positional	0.03	0.05
1	3	C	1246	tight positional	0.02	0.05
3	1	D	614	tight positional	0.06	0.05
3	2	E	614	tight positional	0.03	0.05
3	3	F	614	tight positional	0.04	0.05
1	1	A	7	medium positional	1.4	0.5
1	2	B	7	medium positional	1.38	0.5
1	3	C	7	medium positional	1.28	0.5
2	1	A	19	medium positional	0.68	0.5
3	1	D	190	medium positional	0.95	0.5
3	2	E	190	medium positional	1.11	0.5
3	3	F	190	medium positional	0.95	0.5
1	1	A	105	loose positional	1.36	5
1	2	B	105	loose positional	1.98	5
1	3	C	105	loose positional	1.94	5
1	1	A	1246	tight thermal	0.03	0.5
1	2	B	1246	tight thermal	0.03	0.5
1	3	C	1246	tight thermal	0.03	0.5
3	1	D	614	tight thermal	0.02	0.5
3	2	E	614	tight thermal	0.03	0.5
3	3	F	614	tight thermal	0.02	0.5
1	1	A	7	medium thermal	0.52	2
1	2	B	7	medium thermal	0.57	2
1	3	C	7	medium thermal	0.18	2
2	1	A	19	medium thermal	0.13	2
3	1	D	190	medium thermal	0.13	2
3	2	E	190	medium thermal	0.14	2
3	3	F	190	medium thermal	0.12	2
1	1	A	105	loose thermal	0.43	10
1	2	B	105	loose thermal	0.33	10
1	3	C	105	loose thermal	0.46	10

LS refinement shell

Resolution: 3.2→3.283 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.323	30	-
R_work	0.259	710	-
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	4.6526	1.1886	-0.622	5.6623	-1.2349	5.1809	0.0764	0.2294	0.1106	0.1117	-0.0477	-0.0232	-0.1424	-0.2051	-0.0286	-0.38	0.0468	0.0506	-0.3439	-0.0382	-0.4048	-12.821	5.351	12.371
2	5.2084	-0.9108	-2.3676	5.2604	0.4909	5.1433	0.0902	-0.2351	0.0407	0.0515	-0.1473	0.1605	0.2152	-0.0222	0.0571	-0.4378	-0.1268	-0.0101	-0.265	0.0498	-0.3796	-15.659	-3.169	27.716
3	3.77	0.0313	0.9867	2.4293	0.8958	5.7731	-0.1134	-0.4964	-0.0336	0.106	0.0078	-0.1503	0.4719	0.2843	0.1057	-0.4342	-0.0216	0.0714	-0.2509	0.0415	-0.2572	1.365	-2.306	21.043
4	9.9472	-1.3156	-3.7966	5.0131	3.3502	7.0172	0.3679	-0.9224	1.5461	0.0423	0.1742	-0.4165	-0.4317	0.1416	-0.5422	-0.3138	-0.1405	0.0456	-0.0207	-0.1643	-0.0611	-14.212	13.236	44.317
5	5.4406	-0.4282	0.1119	9.1768	-0.5858	7.0703	0.2465	0.1049	0.7745	0.363	-0.218	-0.2602	-0.554	0.3409	-0.0284	0.0188	-0.0159	0.1649	-0.3669	-0.0309	-0.0651	-12.125	27.845	20.703
6	4.375	1.2053	1.0577	5.1446	-0.9292	2.1687	-0.3056	-0.1828	1.0819	0.5228	-0.1055	0.3143	-0.3353	0.5957	0.4111	-0.1561	-0.2517	0.0416	0.0992	-0.1347	0.2089	10.416	16.413	32.297
7	13.8855	6.7219	1.3142	10.0505	0.4037	5.5437	0.5611	-0.0037	-0.3588	0.3062	-0.3893	0.3275	0.9014	0.0995	-0.1719	-0.27	0.1082	0.1072	-0.0742	-0.0633	-0.1253	-43.086	6.218	45.995
8	31.5594	17.3912	-5.8073	11.7388	-3.0615	12.3165	-1.8929	1.435	-0.8826	-1.6355	0.7162	0.5571	1.1185	0.2047	1.1768	0.4813	-0.0281	-0.1552	0.0244	0.032	0.1701	-14.332	31.709	6.968
9	20.2741	-9.0355	18.0962	4.0268	-8.0648	16.1522	1.8708	-0.0127	2.409	-0.1987	-2.7889	-2.3689	3.0054	-0.8655	0.9182	0.1368	-0.0609	0.1764	0.1801	0.1293	0.5428	25.169	9.908	64.204

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 110
2	X-RAY DIFFRACTION	2	B	1 - 108
3	X-RAY DIFFRACTION	3	C	1 - 112
4	X-RAY DIFFRACTION	4	D	3 - 70
5	X-RAY DIFFRACTION	5	E	3 - 70
6	X-RAY DIFFRACTION	6	F	3 - 70
7	X-RAY DIFFRACTION	7	D	71 - 89
8	X-RAY DIFFRACTION	8	E	71 - 89
9	X-RAY DIFFRACTION	9	F	79 - 89

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi