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- PDB-3s6g: Crystal structures of Seleno-substituted mutant mmNAGS in space g... -

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Basic information

Entry
Database: PDB / ID: 3s6g
TitleCrystal structures of Seleno-substituted mutant mmNAGS in space group P212121
ComponentsN-acetylglutamate kinase / N-acetylglutamate synthase
KeywordsTRANSFERASE / synthase / kinase
Function / homology
Function and homology information


L-glutamate N-acetyltransferase activity / acetylglutamate kinase / acetylglutamate kinase activity / L-arginine biosynthetic process / 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 / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily ...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 / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / MALONATE ION / Acetylglutamate kinase
Similarity search - Component
Biological speciesMaricaulis maris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6681 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 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: N-acetylglutamate kinase / N-acetylglutamate synthase
B: N-acetylglutamate kinase / N-acetylglutamate synthase
X: N-acetylglutamate kinase / N-acetylglutamate synthase
Y: N-acetylglutamate kinase / N-acetylglutamate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,29910
Polymers202,1074
Non-polymers1,1926
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: N-acetylglutamate kinase / N-acetylglutamate synthase
X: N-acetylglutamate kinase / N-acetylglutamate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3145
Polymers101,0532
Non-polymers2603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-23 kcal/mol
Surface area37940 Å2
MethodPISA
3
B: N-acetylglutamate kinase / N-acetylglutamate synthase
Y: N-acetylglutamate kinase / N-acetylglutamate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9855
Polymers101,0532
Non-polymers9323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-10 kcal/mol
Surface area38510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.426, 117.470, 149.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABXY

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


Mass: 50526.684 Da / Num. of mol.: 4 / Mutation: I106M, I294M, L376M
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): B834(DE3)
References: UniProt: Q0ASS9, amino-acid N-acetyltransferase, acetylglutamate kinase

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Non-polymers , 5 types, 90 molecules

#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG3350, 200 mM sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97471, 0.97921, 0.97934
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 23, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.974711
20.979211
30.979341
ReflectionResolution: 2.66→50 Å / Num. obs: 104589 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 36.8
Reflection shellResolution: 2.66→2.73 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.6 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6681→37.969 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.32 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 27.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 3690 3.53 %
Rwork0.1826 --
obs0.1851 104589 95.4 %
all-109628 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.721 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.9617 Å2-0 Å20 Å2
2---5.3741 Å2-0 Å2
3---12.3358 Å2
Refinement stepCycle: LAST / Resolution: 2.6681→37.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13136 0 75 84 13295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913450
X-RAY DIFFRACTIONf_angle_d1.2118278
X-RAY DIFFRACTIONf_dihedral_angle_d16.8824962
X-RAY DIFFRACTIONf_chiral_restr0.082088
X-RAY DIFFRACTIONf_plane_restr0.0072409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6681-2.76350.32523330.27648634X-RAY DIFFRACTION82
2.7635-2.87410.34683380.25569469X-RAY DIFFRACTION89
2.8741-3.00480.34143540.24579666X-RAY DIFFRACTION92
3.0048-3.16320.31023710.222610130X-RAY DIFFRACTION96
3.1632-3.36130.28463740.213410363X-RAY DIFFRACTION98
3.3613-3.62060.26473890.190610439X-RAY DIFFRACTION99
3.6206-3.98460.24793880.172310492X-RAY DIFFRACTION99
3.9846-4.56040.21863720.14210605X-RAY DIFFRACTION100
4.5604-5.74240.24033840.158210534X-RAY DIFFRACTION100
5.7424-37.97290.22773870.17510567X-RAY DIFFRACTION100
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)
10.4992-0.9278-0.51723.1757-0.20942.46580.13790.012-0.0393-0.4190.298-0.6433-0.30950.3466-0.42410.57440.03540.24740.28980.05440.523739.6307-4.020176.3596
21.95180.05280.35831.0990.55711.92840.0038-0.3203-0.20260.0830.0649-0.24130.09360.6674-0.13370.23460.0764-0.00430.4889-0.13270.340443.9491-6.4165105.6313
37.16832.4465-2.00282.59661.04762.29380.1721-0.2603-0.83390.0828-0.0757-0.27620.6903-0.1181-0.05360.45660.0079-0.02620.2592-0.00910.320226.9929-16.031995.3151
41.4033-0.8511-0.78092.24941.03541.4251-0.11680.07970.1290.01090.19560.39610.0572-0.1839-0.01290.0917-0.11040.02870.109-0.00860.31377.3638-15.865478.9031
53.8808-2.5434-0.35972.13720.65592.33270.28030.5881-0.4204-0.1795-0.1872-0.18510.13280.222-0.04570.2498-0.13610.02190.4093-0.12120.413710.8407-29.484470.3854
66.1764-2.5998-1.53474.2645-4.28378.50480.03890.0432-1.4722-0.9492-1.01820.01990.64341.60110.39060.99850.1821-0.43950.7446-0.24681.10277.18938.704781.2783
74.39631.7679-0.68021.6157-1.55390.9828-0.3801-0.27840.53810.12460.08430.1010.38330.14250.14390.6025-0.1715-0.2390.59970.1370.43758.71711.3952107.0387
84.56461.89320.3931.55330.10731.2326-0.1999-0.42840.6823-0.0285-0.07290.2255-0.28350.08160.24150.629-0.1458-0.24620.59820.07090.652878.186421.6717103.0742
91.8762-0.99310.09032.8224-1.88993.0347-0.3603-0.5005-0.2266-0.0750.0964-0.92130.09530.44760.28430.43610.0389-0.19820.53950.18640.887101.767222.869694.5231
102.1803-2.16991.65463.0327-2.32241.6977-0.00740.03560.32850.3346-0.0702-0.47620.03360.40980.13020.3702-0.0226-0.13010.41440.10350.66998.3635.017783.909
110.97080.1138-0.47372.76581.82432.1961-0.473-0.0746-0.145-0.0153-0.36730.5187-0.0818-0.26070.48190.56740.2904-0.15660.66690.06620.589750.3503-17.868373.4201
122.76260.846-2.64723.6175-1.08722.4316-0.17130.30760.0106-0.47780.18290.23520.1463-0.2524-0.00230.1895-0.06170.02790.2049-0.09540.127650.774-6.453945.1849
132.17013.4116-0.01077.39041.13660.274-0.30660.1373-0.0417-0.34570.16040.5572-0.0249-0.29540.10680.4065-0.02330.0110.418-0.07720.310238.9027-24.470851.3111
143.8115-0.5584-0.70151.76160.6874.85960.13180.1751-0.9309-0.1311-0.0188-0.12250.27190.1079-0.11040.1801-0.0175-0.00390.1181-0.0070.49136.2872-46.698663.4434
152.8234-1.0345-1.50934.4528-0.89961.33090.20030.1359-0.17820.3563-0.37460.8062-0.06230.16020.13620.2713-0.16870.1120.2888-0.14410.519922.4333-42.378971.5372
167.5644-2.94841.85191.5551-0.54960.4327-1.8252-0.3420.73681.23790.94060.8483-0.2419-0.78960.72431.55230.22050.13921.2659-0.05420.832867.98720.580274.9256
172.20711.13110.11884.17110.20391.4412-0.07390.1063-0.19450.29910.1495-0.50610.50110.0493-0.0440.4811-0.0232-0.0890.2266-0.06270.407169.84626.418846.4438
181.49242.39430.8214.74350.79921.0614-0.2352-0.0333-0.34620.28310.5728-0.7833-0.20570.5006-0.37540.4608-0.0595-0.02690.4456-0.21150.644979.640325.147252.685
192.0615-1.2180.6172.0287-1.79784.19060.04440.16150.1348-0.15760.07460.28820.3631-0.1358-0.10080.30730.0018-0.0790.1868-0.0510.604573.985547.046168.0939
203.2542-1.4880.9661.6965-1.65172.8131-0.0871-0.01560.10550.422-0.1463-0.58070.0306-0.03880.2510.4299-0.0487-0.10130.2069-0.00090.570685.096945.671680.4602
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 B and resid 5:35)
7X-RAY DIFFRACTION7(chain B and resid 36:204)
8X-RAY DIFFRACTION8(chain B and resid 205:291)
9X-RAY DIFFRACTION9(chain B and resid 292:381)
10X-RAY DIFFRACTION10(chain B and resid 382:439)
11X-RAY DIFFRACTION11(chain X and resid 5:35)
12X-RAY DIFFRACTION12(chain X and resid 36:204)
13X-RAY DIFFRACTION13(chain X and resid 205:291)
14X-RAY DIFFRACTION14(chain X and resid 292:381)
15X-RAY DIFFRACTION15(chain X and resid 382:439)
16X-RAY DIFFRACTION16(chain Y and resid 10:31)
17X-RAY DIFFRACTION17(chain Y and resid 40:204)
18X-RAY DIFFRACTION18(chain Y and resid 205:291)
19X-RAY DIFFRACTION19(chain Y and resid 292:381)
20X-RAY DIFFRACTION20(chain Y and resid 382:440)

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