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- PDB-3s6h: Crystal structure of native mmNAGS/k -

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Basic information

Entry
Database: PDB / ID: 3s6h
TitleCrystal structure of native mmNAGS/k
ComponentsN-acetylglutamate kinase / N-acetylglutamate synthase
KeywordsTRANSFERASE / synthase and 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 / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family ...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 / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 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 / GLUTAMIC ACID / Acetylglutamate kinase
Similarity search - Component
Biological speciesMaricaulis maris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 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 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)202,0318
Polymers200,2024
Non-polymers1,8294
Water1086
1
A: N-acetylglutamate kinase / N-acetylglutamate synthase
X: N-acetylglutamate kinase / N-acetylglutamate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0164
Polymers100,1012
Non-polymers9152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-17 kcal/mol
Surface area38280 Å2
MethodPISA
2
B: N-acetylglutamate kinase / N-acetylglutamate synthase
Y: N-acetylglutamate kinase / N-acetylglutamate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0164
Polymers100,1012
Non-polymers9152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-16 kcal/mol
Surface area38800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.587, 118.211, 152.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 50050.512 Da / Num. of mol.: 4
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): Rossetta 2
References: UniProt: Q0ASS9, amino-acid N-acetyltransferase, acetylglutamate kinase
#2: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG3350, 200 mM NaCl and 100 mM Bis-tris, pH 6.5, 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: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 3, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 38113 / Num. obs: 36398 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.1-3.215.80.607176.2
3.21-3.3460.463184.5
3.34-3.496.30.352194.9
3.49-3.686.90.275199.6
3.68-3.917.30.1951100
3.91-4.217.40.1311100
4.21-4.637.40.0891100
4.63-5.37.40.0841100
5.3-6.677.30.0831100
6.67-506.90.043199.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3S6G

3s6g


Resolution: 3.102→32.8 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.94 / σ(F): 1.36 / Phase error: 32.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2972 1812 4.99 %
Rwork0.1864 --
obs0.1919 36336 95.38 %
all-38099 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.108 Å2 / ksol: 0.274 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.9595 Å2-0 Å20 Å2
2---13.7765 Å2-0 Å2
3---32.736 Å2
Refinement stepCycle: LAST / Resolution: 3.102→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13136 0 116 6 13258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913496
X-RAY DIFFRACTIONf_angle_d1.27818363
X-RAY DIFFRACTIONf_dihedral_angle_d18.0575006
X-RAY DIFFRACTIONf_chiral_restr0.0812109
X-RAY DIFFRACTIONf_plane_restr0.0082412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.102-3.18580.3488990.23562024X-RAY DIFFRACTION74
3.1858-3.27950.3521180.22962228X-RAY DIFFRACTION82
3.2795-3.38530.36151240.25952425X-RAY DIFFRACTION88
3.3853-3.50610.36531390.23672651X-RAY DIFFRACTION96
3.5061-3.64630.33151490.22192728X-RAY DIFFRACTION99
3.6463-3.8120.29491440.19212767X-RAY DIFFRACTION100
3.812-4.01270.31461450.17572759X-RAY DIFFRACTION100
4.0127-4.26360.29281500.15292764X-RAY DIFFRACTION100
4.2636-4.5920.22121460.12682806X-RAY DIFFRACTION100
4.592-5.05260.25321480.14712759X-RAY DIFFRACTION100
5.0526-5.78030.27931450.20322814X-RAY DIFFRACTION100
5.7803-7.26940.36131460.21152851X-RAY DIFFRACTION100
7.2694-32.80190.28861590.18682948X-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)
12.5027-2.3203-0.312.47270.65766.7612-0.04330.35420.2675-0.9924-0.357-0.7087-0.60650.85280.49860.931-0.04450.04120.45490.20740.377139.6296-3.656878.0518
25.19080.19871.12653.63070.00671.50630.2477-0.7849-0.32920.5431-0.3082-0.0531-0.18060.3223-0.00170.4819-0.1031-0.0160.7617-0.10230.272243.9982-5.9495107.258
38.86130.8823-0.87856.16831.47041.80330.5622-0.5258-0.9707-0.0616-0.51980.28150.0843-0.5168-0.05270.42360.0109-0.0390.5453-0.00720.342227.2494-16.046996.9684
42.9499-0.6929-2.30994.15231.10592.3665-0.13090.46920.8415-0.26520.26070.5169-0.2246-0.1943-0.1330.4105-0.1232-0.20270.37160.12510.64826.9748-15.919580.175
56.4351-1.87681.26877.8999-0.09523.5465-0.01331.2312-0.4447-0.0843-0.4604-0.2997-0.26270.52430.46710.4597-0.1945-0.06090.6854-0.13130.522510.7746-29.413271.8239
65.5677-0.5866-1.54865.7429-2.98532.0006-0.34760.6071-1.6229-2.0525-1.3950.73151.46160.37521.42161.40390.4602-0.09671.0906-0.38011.446577.18538.461583.6003
74.88360.63820.09692.1392-1.78993.7003-0.1922-0.46060.68660.17750.05950.13590.05750.19160.11220.8699-0.4171-0.47591.07580.35160.594858.640911.7955108.9472
84.18541.3452-0.54365.25320.41640.36990.0634-0.82930.407-0.05770.1161-0.2676-0.2040.3217-0.03630.8087-0.3492-0.2941.19820.17290.571377.665622.2155105.0845
91.3885-0.70390.47276.5765-0.67431.8230.1389-0.3134-0.24240.2736-0.4298-2.0423-0.18960.45920.48060.637-0.0946-0.28330.77350.6481.6185101.567623.240696.876
102.58751.52370.85856.9481-1.75762.02180.3281-0.3957-0.63620.1781-0.6699-2.24490.26910.50280.42740.6133-0.131-0.05510.7570.57121.277798.499235.192285.7446
114.293-3.969-2.44337.9483-0.46267.0001-0.44720.52780.4330.85050.1239-0.0743-0.38210.11670.35110.67250.3944-0.23590.8274-0.13480.95351.1414-17.746174.7364
122.66160.7979-1.66786.0989-1.48641.6547-0.29160.5320.1083-0.89010.2451-0.17910.2659-0.46990.07620.4422-0.00440.09320.6727-0.28070.343751.1557-6.38846.6006
135.35023.70060.48732.56060.39830.6977-0.07330.2416-0.2381-0.35850.45420.7134-0.1651-0.1128-0.1660.5970.0045-0.03870.7702-0.24560.686639.1143-24.171152.7041
144.9670.6081-0.41454.02290.06156.36320.18480.1807-0.7803-0.2173-0.0242-0.86090.4235-0.122-0.13910.5496-0.0144-0.04890.5173-0.20010.968536.3401-46.543265.1168
154.8076-1.7176-2.85976.6574-2.83724.16460.3698-0.2825-0.69470.7509-0.53931.39220.179-0.17910.18540.4481-0.28790.20710.5031-0.180.833222.557-42.160773.0545
163.3807-2.8431-0.11738.5319-2.6856.1514-1.0529-0.3276-0.2630.38710.39971.0602-2.09010.89981.03781.18180.0277-0.44151.16880.21110.971767.789521.287176.3104
172.79831.431-0.07364.95450.01094.46490.4334-0.1131-0.1867-0.39250.0299-0.6913-0.67130.6532-0.53870.6749-0.07520.06180.5721-0.21611.176570.44615.808749.0093
184.91412.2789-0.90134.50662.07252.8434-0.5550.2566-2.0101-0.98490.452-1.7475-0.39121.15010.13540.8924-0.38780.25780.9483-0.30581.445981.173823.972455.2485
194.857-0.4841.34943.0843-2.49887.4687-0.20490.2694-0.2004-0.32620.11310.86930.4083-0.55560.0810.40740.04270.02410.29010.03740.650174.704247.198169.1827
203.9284-0.48290.21894.5008-1.79394.82950.038-0.20790.1870.9081-0.2119-0.4765-0.3085-0.22950.16750.8358-0.0716-0.06040.47770.04520.670485.260145.788181.7708
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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