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

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Basic information

Entry
Database: PDB / ID: 2jj4
TitleThe complex of PII and acetylglutamate kinase from Synechococcus elongatus PCC7942
Components
  • ACETYLGLUTAMATE KINASE
  • NITROGEN REGULATORY PROTEIN P-II
KeywordsTRANSCRIPTION / 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 activity / acetylglutamate kinase / arginine biosynthetic process via ornithine / regulation of nitrogen utilization / enzyme regulator activity / phosphorylation / nucleotide binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II ...N-Acetyl-L-glutamate kinase, cyclic / Acetylglutamate kinase ArgB / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Acetylglutamate kinase family / Glutamate/acetylglutamate kinase / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Acetylglutamate kinase-like / Carbamate kinase / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Amino acid kinase family / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-ACETYL-L-GLUTAMATE / Nitrogen regulatory protein P-II / Acetylglutamate kinase
Similarity search - Component
Biological speciesSYNECHOCOCCUS ELONGATUS (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsLlacer, J.L. / Marco-Marin, C. / Gil-Ortiz, F. / Fita, I. / Rubio, V.
CitationJournal: 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
DepositionJul 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,0848
Polymers140,7056
Non-polymers3782
Water0
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


Theoretical massNumber of molelcules
Total (without water)282,16716
Polymers281,41012
Non-polymers7574
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area40700 Å2
ΔGint-166.2 kcal/mol
Surface area106620 Å2
MethodPQS
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 number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12D
22E
32F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 85
2111B1 - 85
3111C1 - 85
1214A289 - 300
2214B289 - 300
3214C289 - 300
1314A215 - 224
2314B215 - 224
3314C215 - 224
1411A225 - 289
2411B225 - 289
3411C225 - 289
1511A145 - 214
2511B145 - 214
3511C145 - 214
1614A144
2614B144
3614C144
1715A86 - 93
2715B86 - 93
3715C86 - 93
1811A94 - 143
2811B94 - 143
3811C94 - 143
1121D1 - 25
2121E1 - 25
3121F1 - 25
1226D37 - 42
2226E37 - 42
3226F37 - 42
1324D43 - 47
2324E43 - 47
3324F43 - 47
1421D48 - 100
2421E48 - 100
3421F48 - 100
1523D101 - 103
2523E101 - 103
3523F101 - 103
1621D104 - 107
2621E104 - 107
3621F104 - 107
1724D26 - 28
2724E26 - 28
3724F26 - 28
1821D29 - 36
2821E29 - 36
3821F29 - 36
1926D108 - 112
2926E108 - 112
3926F108 - 112

NCS ensembles :
ID
1
2

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

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Components

#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 (unknown) / 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 (unknown) / 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 / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO5
Sequence detailsN-TERMINALLY HIS-TAGGED (N-TERMINAL EXTRA SEQUENCE MGSSHHHHHHSSGLVPRGSH)

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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: 2.3 Å3/Da / Density % sol: 46.3 % / Description: NONE
Crystal growpH: 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

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

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2BTY AND 1QY7
Resolution: 3.46→50 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 877 5.1 %RANDOM
Rwork0.233 ---
obs0.236 16428 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.37 Å2
Baniso -1Baniso -2Baniso -3
1--3.43 Å20 Å20 Å2
2---1.27 Å20 Å2
3---4.71 Å2
Refinement stepCycle: LAST / Resolution: 3.46→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8522 0 26 0 8548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228662
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.96511765
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5551177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50924.379338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.189151365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7921563
X-RAY DIFFRACTIONr_chiral_restr0.0730.21410
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026534
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.24072
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.25975
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3121.55945
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.57129281
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.58732939
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.1134.52484
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
11A1575tight positional0.020.05
12B1575tight positional0.030.05
13C1575tight positional0.020.05
21D614tight positional0.020.05
22E614tight positional0.020.05
23F614tight positional0.020.05
11A64medium positional0.330.5
12B64medium positional0.550.5
13C64medium positional0.480.5
21D69medium positional0.350.5
22E69medium positional0.330.5
23F69medium positional0.270.5
11A10loose positional1.25
12B10loose positional0.535
13C10loose positional1.65
21D45loose positional1.325
22E45loose positional1.455
23F45loose positional2.25
11A1575tight thermal0.030.5
12B1575tight thermal0.030.5
13C1575tight thermal0.020.5
21D614tight thermal0.020.5
22E614tight thermal0.020.5
23F614tight thermal0.020.5
11A64medium thermal0.12
12B64medium thermal0.142
13C64medium thermal0.142
21D69medium thermal0.162
22E69medium thermal0.132
23F69medium thermal0.192
11A10loose thermal0.5310
12B10loose thermal0.410
13C10loose thermal0.8410
21D45loose thermal1.0310
22E45loose thermal0.4210
23F45loose thermal0.7610
LS refinement shellResolution: 3.46→3.55 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.334 61
Rwork0.284 1195
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.05980.2285-0.01082.8470.2831.3694-0.03880.30370.3858-0.4730.0595-0.3893-0.0138-0.127-0.0207-0.07460.00780.1125-0.18470.1421-0.4121-21.01923.776-24.889
21.81070.7169-0.58053.8563-0.62421.8102-0.15670.1913-0.0063-0.82490.23450.450.2036-0.1989-0.0778-0.0966-0.116-0.1793-0.1020.0455-0.3824-43.334-3.192-22.32
31.5357-1.04051.13612.7175-0.94281.45750.03140.1380.1498-0.5201-0.2124-1.59350.22210.07090.1809-0.20850.06050.4977-0.15530.16930.984312.426-5.665-16.538
43.71721.346-0.61053.0713-0.21150.1003-0.13610.663-0.0204-0.86920.0531-0.78750.30580.17470.0830.20980.04130.381-0.1262-0.13560.1073-9.409-30.587-21.725
52.1259-1.84450.98084.6821-1.42612.024-0.02110.2291-0.4728-0.55110.2171-0.11380.2006-0.2662-0.19590.0678-0.14630.0333-0.2197-0.1201-0.2658-28.073-32.452-16.927
63.20732.91991.79343.70161.44745.0545-0.0331-0.01560.68770.4185-0.1477-0.3047-0.41590.23330.1808-0.1240.0528-0.0685-0.37280.01250.1464-14.62437.8694.253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 291
2X-RAY DIFFRACTION2B8 - 291
3X-RAY DIFFRACTION3C7 - 291
4X-RAY DIFFRACTION4D1 - 111
5X-RAY DIFFRACTION5E1 - 108
6X-RAY DIFFRACTION6F1 - 109

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