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- PDB-3s7y: Crystal structure of mmNAGS in Space Group P3121 at 4.3 A resolution -

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Basic information

Entry
Database: PDB / ID: 3s7y
TitleCrystal structure of mmNAGS in Space Group P3121 at 4.3 A resolution
ComponentsN-acetylglutamate kinase / N-acetylglutamate synthase
KeywordsTRANSFERASE / synthase / kinase
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / phosphorylation / cytoplasm
Similarity search - Function
Acetylglutamate kinase ArgB, GNAT domain-containing / N-Acetyl-L-glutamate kinase, fungal-type / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain / NAT, N-acetyltransferase, of N-acetylglutamate synthase / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain profile. / Acetylglutamate kinase family / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...Acetylglutamate kinase ArgB, GNAT domain-containing / N-Acetyl-L-glutamate kinase, fungal-type / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain / NAT, N-acetyltransferase, of N-acetylglutamate synthase / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain profile. / Acetylglutamate kinase family / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Acetylglutamate kinase
Similarity search - Component
Biological speciesMaricaulis maris (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 4.3077 Å
AuthorsShi, D. / Li, Y. / Cabrera-Luque, J. / Jin, Z. / Yu, X. / Allewell, N.M. / Tuchman, M.
CitationJournal: Plos One / Year: 2011
Title: A Novel N-acetylglutamate synthase architecture revealed by the crystal structure of the bifunctional enzyme from Maricaulis maris.
Authors: Shi, D. / Li, Y. / Cabrera-Luque, J. / Jin, Z. / Yu, X. / Zhao, G. / Haskins, N. / Allewell, N.M. / Tuchman, M.
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetylglutamate kinase / N-acetylglutamate synthase
X: N-acetylglutamate kinase / N-acetylglutamate synthase


Theoretical massNumber of molelcules
Total (without water)100,3572
Polymers100,3572
Non-polymers00
Water0
1
A: N-acetylglutamate kinase / N-acetylglutamate synthase
X: N-acetylglutamate kinase / N-acetylglutamate synthase

A: N-acetylglutamate kinase / N-acetylglutamate synthase
X: N-acetylglutamate kinase / N-acetylglutamate synthase


Theoretical massNumber of molelcules
Total (without water)200,7154
Polymers200,7154
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-20 kcal/mol
Surface area40470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.108, 95.108, 253.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 38:83 or resseq 98:296 )
211chain X and (resseq 38:83 or resseq 98:296 )
112chain A and (resseq 297:330 or resseq 333:439 )
212chain X and (resseq 297:330 or resseq 333:439 )

NCS ensembles :
ID
1
2

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Components

#1: Protein N-acetylglutamate kinase / N-acetylglutamate synthase


Mass: 50178.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maricaulis maris (bacteria) / Strain: MCS10 / Gene: argA/B, Mmar10_0365 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0ASS9, amino-acid N-acetyltransferase, acetylglutamate kinase

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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: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 23% PEG400, 100 mM Bis-tris, 1 mM 5-amino-2,4,6-triiodoisophthalic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 22, 2009
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. all: 9544 / Num. obs: 9506 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
4.3-4.455.60.915199.5
4.45-4.635.60.6671100
4.63-4.845.60.683199.6
4.84-5.15.60.483199.9
5.1-5.425.50.428199.9
5.42-5.835.60.34199.9
5.83-6.425.90.2181100
6.42-7.356.40.099199.9
7.35-9.257.10.0351100
9.25-5080.022197.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S6G

3s6g


Resolution: 4.3077→31.131 Å / Occupancy max: 1 / Occupancy min: 0.06 / SU ML: 1.06 / σ(F): 0 / Phase error: 46.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4188 867 9.92 %
Rwork0.274 --
obs0.2885 8736 92.1 %
all-9506 -
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 346.558 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4782 Å2-0 Å20 Å2
2---3.4782 Å2-0 Å2
3---6.9564 Å2
Refinement stepCycle: LAST / Resolution: 4.3077→31.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6675 0 0 0 6675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156803
X-RAY DIFFRACTIONf_angle_d2.4569251
X-RAY DIFFRACTIONf_dihedral_angle_d17.5592489
X-RAY DIFFRACTIONf_chiral_restr0.1441062
X-RAY DIFFRACTIONf_plane_restr0.0111224
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1810X-RAY DIFFRACTIONPOSITIONAL
12X1810X-RAY DIFFRACTIONPOSITIONAL0.103
21A1126X-RAY DIFFRACTIONPOSITIONAL
22X1126X-RAY DIFFRACTIONPOSITIONAL0.104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.3077-4.57680.51751320.45241179X-RAY DIFFRACTION84
4.5768-4.92890.44951230.36341188X-RAY DIFFRACTION86
4.9289-5.42250.47871440.33191244X-RAY DIFFRACTION90
5.4225-6.20180.63621470.40391332X-RAY DIFFRACTION94
6.2018-7.79330.45281570.27051413X-RAY DIFFRACTION98
7.7933-31.13220.35171640.21011513X-RAY DIFFRACTION99
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)
13.3682-1.61320.09150.7721-0.1372.0637-2.4961.91790.9271-5.0014-1.2577-1.8789-1.88030.64231.43144.6456-0.411.81553.03460.30844.7294-12.8235-16.42518.9618
22.601-1.3555-3.67141.6080.09783.0718-0.5567-2.11761.2862-0.0853.0639-0.25311.9171-1.4191-0.29131.6111-0.862-0.37882.245-1.00081.499610.4024-34.250322.5536
32.09480.63265.20282.58050.16624.8384-1.01021.83972.26613.1854-1.58783.23321.4556-0.63840.90351.3727-0.10580.54271.2381-1.17261.6971-0.9689-26.785239.9297
45.0034-0.5125-3.27515.0946-5.10962.2088-0.46090.8029-0.54-1.9414-1.0999-1.90284.1421-0.3256-0.02721.8264-1.4259-0.19921.5589-0.84421.9403-9.5158-3.686651.4367
51.8913-7.96927.17928.0101-6.92662.15571.4589-0.433-1.4553-3.15162.73420.1444-0.1401-1.52920.60531.6536-1.17390.72363.1581-0.68020.91-26.1328-6.454251.8474
63.53431.45664.95651.68960.31272.0199-0.13081.0948-1.3094-3.63431.4823-0.01892.12125.3689-0.86143.778-0.3584-1.95933.2044-0.9142.0287-26.2009-25.447712.9072
73.82810.45271.06082.36921.32742.4322.4264-0.57720.02760.7219-0.5179-0.47810.82850.94120.30141.7772-0.360.87482.0846-0.26991.0271-37.7912-0.8056-1.0305
82.3853-3.4215-0.15761.88182.03172.3795-1.3177-4.59871.0984-5.24614.83582.6008-2.69671.0284-1.19081.051-1.00780.16763.8716-0.16251.0898-42.1343-5.54420.2605
94.41010.1991-2.71553.4125-0.36555.05261.59671.10943.1654-6.26161.29411.5461-2.247-0.7810.06851.6081-2.986-1.3956-1.2718-1.58311.2639-49.1025-23.081437.2228
101.77311.8042-7.27317.95544.74814.7555-1.6256-3.41626.6399-0.84515.2152-1.37981.5389-0.75420.16870.6382-0.9135-0.37195.35941.92791.7897-36.8524-19.272548.3895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:35)
2X-RAY DIFFRACTION2(chain A and resid 36:204)
3X-RAY DIFFRACTION3(chain A and resid 205:291)
4X-RAY DIFFRACTION4(chain A and resid 292:381)
5X-RAY DIFFRACTION5(chain A and resid 382:440)
6X-RAY DIFFRACTION6(chain X and resid 5:35)
7X-RAY DIFFRACTION7(chain X and resid 36:204)
8X-RAY DIFFRACTION8(chain X and resid 205:291)
9X-RAY DIFFRACTION9(chain X and resid 292:381)
10X-RAY DIFFRACTION10(chain X and resid 382:439)

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