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- PDB-4usj: N-acetylglutamate kinase from Arabidopsis thaliana in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4usj
TitleN-acetylglutamate kinase from Arabidopsis thaliana in complex with PII from Chlamydomonas reinhardtii
Components
  • ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
  • NITROGEN REGULATORY PROTEIN PII
KeywordsTRANSFERASE / NAGK / NITROGEN ASSIMILATION / Q-LOOP / C-TERMINAL EXTENSION / PROTEIN-PROTEIN COMPLEX / REGULATION OF ARGININE METABOLISM / SIGNALING PROTEIN
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / chloroplast thylakoid / arginine biosynthetic process via ornithine / regulation of nitrogen utilization / arginine binding / chloroplast stroma / enzyme regulator activity / chloroplast / phosphorylation ...acetylglutamate kinase / acetylglutamate kinase activity / chloroplast thylakoid / arginine biosynthetic process via ornithine / regulation of nitrogen utilization / arginine binding / chloroplast stroma / enzyme regulator activity / chloroplast / phosphorylation / ATP binding / cytosol
Similarity search - Function
N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein PII / P-II protein family profile. ...N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Acetylglutamate kinase family / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein PII / P-II protein family profile. / Carbamate kinase / Acetylglutamate kinase-like / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ARGININE / ADENOSINE-5'-TRIPHOSPHATE / GLUTAMINE / N-ACETYL-L-GLUTAMATE / N-ACETYL-L-GLUTAMYL 5-PHOSPHATE / Nitrogen regulatory protein PII / Acetylglutamate kinase, chloroplastic
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
CHLAMYDOMONAS REINHARDTII (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsChellamuthu, V.R. / Forchhammer, K. / Hartmann, M.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: A Widespread Glutamine-Sensing Mechanism in the Plant Kingdom.
Authors: Chellamuthu, V.R. / Ermilova, E. / Lapina, T. / Luddecke, J. / Minaeva, E. / Herrmann, C. / Hartmann, M.D. / Forchhammer, K.
History
DepositionJul 8, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
B: ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
C: NITROGEN REGULATORY PROTEIN PII
D: NITROGEN REGULATORY PROTEIN PII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,61016
Polymers100,9944
Non-polymers2,61512
Water1,874104
1
A: ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
B: ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
C: NITROGEN REGULATORY PROTEIN PII
D: NITROGEN REGULATORY PROTEIN PII
hetero molecules

A: ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
B: ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
C: NITROGEN REGULATORY PROTEIN PII
D: NITROGEN REGULATORY PROTEIN PII
hetero molecules

A: ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
B: ACETYLGLUTAMATE KINASE, CHLOROPLASTIC
C: NITROGEN REGULATORY PROTEIN PII
D: NITROGEN REGULATORY PROTEIN PII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,83048
Polymers302,98312
Non-polymers7,84636
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)171.430, 171.430, 171.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11C-2003-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110C
210D
111C
211D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A20 - 40
2111B20 - 40
1121A53 - 78
2121B53 - 78
1131A80 - 84
2131B80 - 84
1141A86 - 87
2141B86 - 87
1151A95 - 146
2151B95 - 146
1161A155 - 213
2161B155 - 213
1171A227 - 242
2171B227 - 242
1181A255 - 273
2181B255 - 273
1191A278 - 294
2191B278 - 294
11101C5 - 125
21101D5 - 125
11111C126 - 150
21111D126 - 150

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.193227, -0.221674, -0.955784), (-0.242087, -0.954797, 0.172503), (-0.950819, 0.198051, -0.238157)121.03334, 124.15719, 121.08631
3given(1), (1), (1)
4given(0.207089, -0.221977, -0.952806), (-0.224809, -0.958654, 0.174478), (-0.952142, 0.178067, -0.24843)119.6663, 122.81613, 123.24798
5given(1), (1), (1)
6given(0.144626, -0.178559, -0.973242), (-0.209246, -0.966858, 0.146293), (-0.967109, 0.182489, -0.177195)121.4153, 123.21717, 121.39548
7given(1), (1), (1)
8given(0.173375, -0.191008, -0.966156), (-0.297998, -0.945201, 0.13339), (-0.93869, 0.264786, -0.220795)120.3942, 128.10347, 112.5973
9given(1), (1), (1)
10given(0.161126, -0.208993, -0.964552), (-0.194931, -0.964808, 0.176485), (-0.967492, 0.159585, -0.196194)122.55265, 120.99054, 123.90138
11given(1), (1), (1)
12given(0.187485, -0.212382, -0.959033), (-0.215465, -0.961459, 0.170797), (-0.958345, 0.174616, -0.22602)120.76839, 122.31087, 123.25632
13given(1), (1), (1)
14given(0.316037, -0.173507, -0.932746), (-0.442892, -0.89642, 0.016688), (-0.839028, 0.407832, -0.360147)105.23013, 145.07159, 100.15273
15given(1), (1), (1)
16given(0.237123, -0.190731, -0.952573), (-0.322815, -0.94029, 0.107914), (-0.916277, 0.281916, -0.284535)114.72282, 133.22101, 113.91508
17given(1), (1), (1)
18given(0.213754, -0.156568, -0.964259), (-0.246299, -0.963823, 0.101898), (-0.945329, 0.215715, -0.244583)114.89294, 127.86747, 119.78382
19given(1), (1), (1)
20given(0.187458, -0.235018, -0.953743), (-0.235582, -0.953374, 0.188623), (-0.953604, 0.189326, -0.234083)122.32534, 122.29313, 122.23766
21given(1), (1), (1)
22given(0.189358, -0.239889, -0.952154), (-0.228442, -0.953852, 0.194886), (-0.954965, 0.180609, -0.23542)122.40028, 121.86073, 122.75237

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein ACETYLGLUTAMATE KINASE, CHLOROPLASTIC / / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / ATNAGK / ACETYLGLUTAMATE KINASE


Mass: 33425.551 Da / Num. of mol.: 2 / Fragment: RESIDUES 51-347
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9SCL7, acetylglutamate kinase
#2: Protein NITROGEN REGULATORY PROTEIN PII


Mass: 17071.666 Da / Num. of mol.: 2 / Fragment: RESIDUES 63-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLAMYDOMONAS REINHARDTII (plant) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A8JI83

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Non-polymers , 8 types, 116 molecules

#3: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-NLG / N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO5
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-X2W / N-ACETYL-L-GLUTAMYL 5-PHOSPHATE / N-ACETYL-5-OXO-5-(PHOSPHONOOXY)-L-NORVALINE


Type: L-peptide linking / Mass: 269.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12NO8P
#8: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#9: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growDetails: 200 MM NACL, 100 MM NA/K PHOSPHATE, PH 6.2, 50% (V/V) PEG 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→39.3 Å / Num. obs: 39062 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.6
Reflection shellResolution: 2.85→2.96 Å / Redundancy: 5.09 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.33 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RD5

2rd5


Resolution: 2.85→39.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 19.205 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.22002 2027 5.2 %RANDOM
Rwork0.18869 ---
obs0.1903 37036 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.932 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.85→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6281 0 166 104 6551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196550
X-RAY DIFFRACTIONr_bond_other_d0.0020.026484
X-RAY DIFFRACTIONr_angle_refined_deg2.0382.0098879
X-RAY DIFFRACTIONr_angle_other_deg0.992314896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7985846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93523.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.438151125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9641548
X-RAY DIFFRACTIONr_chiral_restr0.0920.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217297
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021350
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1874tight positional0.030.05
11A258tight positional0.040.05
12B1874tight positional0.030.05
12B258tight positional0.040.05
11A352tight thermal3.030.5
12B352tight thermal3.030.5
21A376tight thermal2.80.5
22B376tight thermal2.80.5
31A96tight thermal4.460.5
32B96tight thermal4.460.5
41A36tight thermal2.290.5
42B36tight thermal2.290.5
51A755tight thermal2.210.5
52B755tight thermal2.210.5
61A848tight thermal2.710.5
62B848tight thermal2.710.5
71A237tight thermal6.420.5
72B237tight thermal6.420.5
81A281tight thermal2.850.5
82B281tight thermal2.850.5
91A236tight thermal4.330.5
92B236tight thermal4.330.5
101C1874tight thermal2.120.5
102D1874tight thermal2.120.5
111C258tight thermal3.070.5
112D258tight thermal3.070.5
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 144 -
Rwork0.233 2662 -
obs--97.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.9216-0.56530.27712.2716-0.74352.02050.01310.31170.0739-0.4501-0.0533-0.09720.07080.06550.04020.1195-0.0141-0.02050.1271-0.00730.078480.116434.518448.5005
20.7358-0.34220.33623.3941-0.59971.1255-0.00250.0177-0.0550.1303-0.0622-0.75490.06750.39340.06470.1058-0.0349-0.06160.20870.02610.201782.927379.717941.2811
30.9938-0.27970.21872.1295-0.74292.4509-0.031-0.00470.2838-0.0007-0.0517-0.4207-0.01880.42630.08280.0558-0.0545-0.02550.1609-0.01180.159793.381582.571176.4644
42.3388-0.52160.93161.9817-0.4731.3885-0.00290.3739-0.0937-0.3672-0.0373-0.02510.3458-0.0310.04020.1732-0.04450.00970.1157-0.05820.04647.527635.988130.8051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 304
2X-RAY DIFFRACTION2B17 - 303
3X-RAY DIFFRACTION3C3 - 303
4X-RAY DIFFRACTION4D3 - 303

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