PDB-2jj4: The complex of PII and acetylglutamate kinase from Synechococcus ...

ID or keywords:

Entry

Database: PDB / ID: 2jj4

Title

The complex of PII and acetylglutamate kinase from Synechococcus elongatus PCC7942

Components

ACETYLGLUTAMATE KINASE
NITROGEN REGULATORY PROTEIN P-II

Keywords

TRANSCRIPTION / TRANSFERASE / CYANOBACTERIA / ACETYLGLUTAMATE / PHOSPHORYLATION / PII SIGNAL PROTEIN / TRANSCRIPTION REGULATION / N-ACETYL-L-GLUTAMATE KINASE / NUCLEOTIDE-BINDING / ARGININE INHIBITION / ARGININE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / GLNB / KINASE / TRIMER / HEXAMER / ATP-BINDING

Function / homology

Function and homology information

acetylglutamate kinase / acetylglutamate kinase activity / L-arginine biosynthetic process via ornithine / regulation of nitrogen utilization / L-arginine biosynthetic process / enzyme regulator activity / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function

Biological species

SYNECHOCOCCUS ELONGATUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.46 Å

Authors

Llacer, J.L. / Marco-Marin, C. / Gil-Ortiz, F. / Fita, I. / Rubio, V.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: The Crystal Structure of the Complex of Pii and Acetylglutamate Kinase Reveals How Pii Controls the Storage of Nitrogen as Arginine
Authors: Llacer, J.L. / Contreras, A. / Forchhammer, K. / Marco-Marin, C. / Gil-Ortiz, F. / Maldonado, R. / Fita, I. / Rubio, V.

History

Deposition	Jul 4, 2007	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 16, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Dec 13, 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	2jj4.cif.gz	222.5 KB	Display	PDBx/mmCIF format
PDB format	pdb2jj4.ent.gz	176.3 KB	Display	PDB format
PDBx/mmJSON format	2jj4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2jj4_validation.pdf.gz	474.7 KB	Display	wwPDB validaton report
Full document	2jj4_full_validation.pdf.gz	494.1 KB	Display
Data in XML	2jj4_validation.xml.gz	41 KB	Display
Data in CIF	2jj4_validation.cif.gz	55.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jj/2jj4 ftp://data.pdbj.org/pub/pdb/validation_reports/jj/2jj4	HTTPS FTP

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Related structure data

Related structure data	2v5hC 1qy7S 2btyS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2v5h-d 3134 2zi8-1 5hcf-d 1mkd-2 1tf7-d 3x2r-d 4q79-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
Related items in Molecule of the Month	#215 - Nov 2017 Aspartate Transcarbamoylase similarity (1)

Deposited unit

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

C: ACETYLGLUTAMATE KINASE

D: NITROGEN REGULATORY PROTEIN P-II

E: NITROGEN REGULATORY PROTEIN P-II

F: NITROGEN REGULATORY PROTEIN P-II

hetero molecules

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

1

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

C: ACETYLGLUTAMATE KINASE

D: NITROGEN REGULATORY PROTEIN P-II

E: NITROGEN REGULATORY PROTEIN P-II

F: NITROGEN REGULATORY PROTEIN P-II

hetero molecules

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

C: ACETYLGLUTAMATE KINASE

D: NITROGEN REGULATORY PROTEIN P-II

E: NITROGEN REGULATORY PROTEIN P-II

F: NITROGEN REGULATORY PROTEIN P-II

hetero molecules

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

Unit cell

Length a, b, c (Å)	106.901, 149.539, 162.205
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	1 - 85
2	1	1	1	B	1 - 85
3	1	1	1	C	1 - 85
1	2	1	4	A	289 - 300
2	2	1	4	B	289 - 300
3	2	1	4	C	289 - 300
1	3	1	4	A	215 - 224
2	3	1	4	B	215 - 224
3	3	1	4	C	215 - 224
1	4	1	1	A	225 - 289
2	4	1	1	B	225 - 289
3	4	1	1	C	225 - 289
1	5	1	1	A	145 - 214
2	5	1	1	B	145 - 214
3	5	1	1	C	145 - 214
1	6	1	4	A	144
2	6	1	4	B	144
3	6	1	4	C	144
1	7	1	5	A	86 - 93
2	7	1	5	B	86 - 93
3	7	1	5	C	86 - 93
1	8	1	1	A	94 - 143
2	8	1	1	B	94 - 143
3	8	1	1	C	94 - 143
1	1	2	1	D	1 - 25
2	1	2	1	E	1 - 25
3	1	2	1	F	1 - 25
1	2	2	6	D	37 - 42
2	2	2	6	E	37 - 42
3	2	2	6	F	37 - 42
1	3	2	4	D	43 - 47
2	3	2	4	E	43 - 47
3	3	2	4	F	43 - 47
1	4	2	1	D	48 - 100
2	4	2	1	E	48 - 100
3	4	2	1	F	48 - 100
1	5	2	3	D	101 - 103
2	5	2	3	E	101 - 103
3	5	2	3	F	101 - 103
1	6	2	1	D	104 - 107
2	6	2	1	E	104 - 107
3	6	2	1	F	104 - 107
1	7	2	4	D	26 - 28
2	7	2	4	E	26 - 28
3	7	2	4	F	26 - 28
1	8	2	1	D	29 - 36
2	8	2	1	E	29 - 36
3	8	2	1	F	29 - 36
1	9	2	6	D	108 - 112
2	9	2	6	E	108 - 112
3	9	2	6	F	108 - 112

NCS ensembles :

ID
1
2

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.498, -0.341, 0.797), (-0.345, -0.766, -0.543), (0.795, -0.546, 0.264)	-25.86395, -5.84928, 13.77266
2	given	(-0.503, 0.346, -0.792), (0.34, -0.763, -0.55), (-0.795, -0.546, 0.266)	-25.9664, 5.84689, -13.67919
3	given	(-0.499, -0.342, 0.796), (0.336, 0.771, 0.541), (-0.799, 0.538, -0.27)	-25.76263, 5.82089, -14.07029
4	given	(-0.502, 0.339, -0.796), (0.347, -0.764, -0.544), (-0.792, -0.549, 0.266)	-25.92554, 6.02547, -13.70219

#1: Protein	ACETYLGLUTAMATE KINASE / NAG KINASE / AGK / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE Mass: 34492.391 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 7942 / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q6V1L5, acetylglutamate kinase
#2: Protein	NITROGEN REGULATORY PROTEIN P-II / PII SIGNAL TRANSDUCING PROTEIN / PII 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 / References: UniProt: P0A3F4
#3: Chemical	ChemComp-NLG / N-ACETYL-L-GLUTAMATE Mass: 189.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₁NO₅
Sequence details	N-TERMINALLY HIS-TAGGED (N-TERMINAL EXTRA SEQUENCE MGSSHHHHHHSSGLVPRGSH)

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.3 % / Description: NONE
Crystal grow	pH: 6.5 Details: 0.1M SODIUM CACODYLATE PH 6.5, 0.25M MAGNESIUM ACETATE, 10%(WT/VOL) POLYETHYLENE GLYCOL 8K, 20MM ACETYLGLUTAMATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
Detector	Type: ADSC CCD Q4R / Detector: CCD / Date: Dec 7, 2005 / Details: TOROIDAL MIRROR
Radiation	Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 3.46→54.07 Å / Num. obs: 17338 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / B_iso Wilson estimate: 81.2 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 6.3
Reflection shell	Resolution: 3.46→3.65 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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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 ENTRIES 2BTY AND 1QY7

2bty

1qy7

Resolution: 3.46→50 Å / Cor.coef. F_o:F_c: 0.897 / Cor.coef. F_o:F_c free: 0.847 / SU B: 86.884 / SU ML: 0.626 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.748 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.294	877	5.1 %	RANDOM
R_work	0.233	-	-	-
obs	0.236	16428	99.9 %	-

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: 73.37 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-3.43 Å²	0 Å²	0 Å²
2-	-	-1.27 Å²	0 Å²
3-	-	-	4.71 Å²

Refinement step

Cycle: LAST / Resolution: 3.46→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8522	0	26	0	8548

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	8662
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.132	1.965	11765
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.55	5	1177
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.509	24.379	338
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.189	15	1365
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.792	15	63
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	1410
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6534
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	4072
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	5975
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.134	0.2	290
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	0.192	0.2	98
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.101	0.2	15
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	0.312	1.5	5945
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.571	2	9281
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.587	3	2939
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.113	4.5	2484
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	1575	tight positional	0.02	0.05
1	2	B	1575	tight positional	0.03	0.05
1	3	C	1575	tight positional	0.02	0.05
2	1	D	614	tight positional	0.02	0.05
2	2	E	614	tight positional	0.02	0.05
2	3	F	614	tight positional	0.02	0.05
1	1	A	64	medium positional	0.33	0.5
1	2	B	64	medium positional	0.55	0.5
1	3	C	64	medium positional	0.48	0.5
2	1	D	69	medium positional	0.35	0.5
2	2	E	69	medium positional	0.33	0.5
2	3	F	69	medium positional	0.27	0.5
1	1	A	10	loose positional	1.2	5
1	2	B	10	loose positional	0.53	5
1	3	C	10	loose positional	1.6	5
2	1	D	45	loose positional	1.32	5
2	2	E	45	loose positional	1.45	5
2	3	F	45	loose positional	2.2	5
1	1	A	1575	tight thermal	0.03	0.5
1	2	B	1575	tight thermal	0.03	0.5
1	3	C	1575	tight thermal	0.02	0.5
2	1	D	614	tight thermal	0.02	0.5
2	2	E	614	tight thermal	0.02	0.5
2	3	F	614	tight thermal	0.02	0.5
1	1	A	64	medium thermal	0.1	2
1	2	B	64	medium thermal	0.14	2
1	3	C	64	medium thermal	0.14	2
2	1	D	69	medium thermal	0.16	2
2	2	E	69	medium thermal	0.13	2
2	3	F	69	medium thermal	0.19	2
1	1	A	10	loose thermal	0.53	10
1	2	B	10	loose thermal	0.4	10
1	3	C	10	loose thermal	0.84	10
2	1	D	45	loose thermal	1.03	10
2	2	E	45	loose thermal	0.42	10
2	3	F	45	loose thermal	0.76	10

LS refinement shell

Resolution: 3.46→3.55 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.334	61
R_work	0.284	1195

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	4.0598	0.2285	-0.0108	2.847	0.283	1.3694	-0.0388	0.3037	0.3858	-0.473	0.0595	-0.3893	-0.0138	-0.127	-0.0207	-0.0746	0.0078	0.1125	-0.1847	0.1421	-0.4121	-21.019	23.776	-24.889
2	1.8107	0.7169	-0.5805	3.8563	-0.6242	1.8102	-0.1567	0.1913	-0.0063	-0.8249	0.2345	0.45	0.2036	-0.1989	-0.0778	-0.0966	-0.116	-0.1793	-0.102	0.0455	-0.3824	-43.334	-3.192	-22.32
3	1.5357	-1.0405	1.1361	2.7175	-0.9428	1.4575	0.0314	0.138	0.1498	-0.5201	-0.2124	-1.5935	0.2221	0.0709	0.1809	-0.2085	0.0605	0.4977	-0.1553	0.1693	0.9843	12.426	-5.665	-16.538
4	3.7172	1.346	-0.6105	3.0713	-0.2115	0.1003	-0.1361	0.663	-0.0204	-0.8692	0.0531	-0.7875	0.3058	0.1747	0.083	0.2098	0.0413	0.381	-0.1262	-0.1356	0.1073	-9.409	-30.587	-21.725
5	2.1259	-1.8445	0.9808	4.6821	-1.4261	2.024	-0.0211	0.2291	-0.4728	-0.5511	0.2171	-0.1138	0.2006	-0.2662	-0.1959	0.0678	-0.1463	0.0333	-0.2197	-0.1201	-0.2658	-28.073	-32.452	-16.927
6	3.2073	2.9199	1.7934	3.7016	1.4474	5.0545	-0.0331	-0.0156	0.6877	0.4185	-0.1477	-0.3047	-0.4159	0.2333	0.1808	-0.124	0.0528	-0.0685	-0.3728	0.0125	0.1464	-14.624	37.869	4.253

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 291
2	X-RAY DIFFRACTION	2	B	8 - 291
3	X-RAY DIFFRACTION	3	C	7 - 291
4	X-RAY DIFFRACTION	4	D	1 - 111
5	X-RAY DIFFRACTION	5	E	1 - 108
6	X-RAY DIFFRACTION	6	F	1 - 109

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