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- PDB-2r8v: Native structure of N-acetylglutamate synthase from Neisseria gon... -

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Basic information

Entry
Database: PDB / ID: 2r8v
TitleNative structure of N-acetylglutamate synthase from Neisseria gonorrhoeae
ComponentsPutative acetylglutamate synthase
KeywordsTRANSFERASE / Protein-AcCoA complex
Function / homology
Function and homology information


acetyl-CoA:L-glutamate N-acetyltransferase activity / methione N-acyltransferase activity / amino-acid N-acetyltransferase / arginine biosynthetic process / cytoplasm
Similarity search - Function
Amino-acid N-acetyltransferase / N-acetylglutamate synthase, kinase-like domain / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...Amino-acid N-acetyltransferase / N-acetylglutamate synthase, kinase-like domain / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Acetyltransferase (GNAT) 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
ACETYL COENZYME *A / Amino-acid acetyltransferase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsShi, D. / Sagar, V. / Jin, Z. / Yu, X. / Caldovic, L. / Morizono, H. / Allewell, N.M. / Tuchman, M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The crystal structure of N-acetyl-L-glutamate synthase from Neisseria gonorrhoeae provides insights into mechanisms of catalysis and regulation.
Authors: Shi, D. / Sagar, V. / Jin, Z. / Yu, X. / Caldovic, L. / Morizono, H. / Allewell, N.M. / Tuchman, M.
History
DepositionSep 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acetylglutamate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0452
Polymers49,2351
Non-polymers8101
Water2,108117
1
A: Putative acetylglutamate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)300,27012
Polymers295,4136
Non-polymers4,8576
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_666-y+1,-x+1,-z+11
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation6_556x,x-y,-z+11
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation5_656-x+y+1,y,-z+11
Buried area28380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.661, 98.661, 89.755
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11A-492-

HOH

21A-533-

HOH

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Components

#1: Protein Putative acetylglutamate synthase


Mass: 49235.492 Da / Num. of mol.: 1 / Mutation: V312I, D336N, P427S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: ATCC 53420 / Gene: argA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5FAK7, amino-acid N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 25% PEG3350, 100mM CsCl, 100 MM sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 18, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 17454 / Num. obs: 17297 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 30.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.872 / SU ML: 0.222 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.537 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. For this and related entry 2R98, The structures were solved by MAD datasets collect at three wavelengths at Se edge. After the first ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. For this and related entry 2R98, The structures were solved by MAD datasets collect at three wavelengths at Se edge. After the first structural model was built, the refinements were carried on against different datasets since they are in same space group and a similar unit cell.
RfactorNum. reflection% reflectionSelection details
Rfree0.25234 872 5 %RANDOM
Rwork0.19153 ---
obs0.19438 16396 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.591 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20.88 Å20 Å2
2--1.76 Å20 Å2
3----2.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 51 117 3395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0411.9744514
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6725422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20122.763152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.87415541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5921534
X-RAY DIFFRACTIONr_chiral_restr0.1460.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.020.022530
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3040.31634
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3370.52294
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.5202
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.381
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3170.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8931.52141
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.70923316
X-RAY DIFFRACTIONr_scbond_it6.51331313
X-RAY DIFFRACTIONr_scangle_it8.664.51198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 73 -
Rwork0.282 1185 -
obs--98.13 %
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)
11.609-0.4794-0.18194.7133-0.93430.68520.18650.0384-0.1290.0039-0.16630.47750.0584-0.0508-0.02020.2131-0.062-0.08980.15250.05750.175318.647724.470939.5797
224.51318.24-10.65619.111310.841342.07990.6910.16633.1976-0.19850.87120.75280.985-1.9203-1.5622-0.15960.1773-0.0949-0.47610.47080.59385.620248.736728.3505
31.58070.8769-0.74010.5179-0.08053.81130.14380.02770.3444-0.067-0.25810.41440.0872-0.00040.11430.13150.0313-0.0060.05280.07490.275414.998745.341440.0873
41.8709-0.02930.85221.7114-0.52481.38290.12050.09970.2094-0.0602-0.11240.0865-0.09610.0987-0.00810.21680.013-0.00010.14090.07140.128625.066339.618532.6298
59.1742-1.57040.08088.0736-2.82016.67380.40050.3823-0.4683-0.5008-0.31660.65470.0069-0.4456-0.08390.01920.0635-0.17980.1202-0.07050.057510.179524.646118.9414
64.2612-0.2996-2.25722.51790.29235.4936-0.03630.0645-0.5625-0.1599-0.29950.17990.17830.09090.33590.24280.086-0.12140.15860.00120.21619.044625.736826.4188
73.5963-1.8621-3.36266.541-3.121411.27580.17520.0595-0.75570.1049-0.02060.55210.4779-0.6637-0.15460.131-0.0357-0.17120.02420.01280.147516.693117.127431.418
85.6107-1.87992.29116.8141-2.11445.1236-0.30810.44780.391-0.05210.1066-0.3468-0.95450.43890.20150.2467-0.14830.07990.021-0.07890.131738.72015.96383.0783
922.5225-4.17926.714812.3199-14.460717.1288-0.5392-0.9911-1.3103-1.68030.6417-0.67330.32911.511-0.10250.1419-0.30260.26230.0096-0.4802-0.062337.3237-3.6272-3.5869
102.33930.90841.35725.22120.08773.5562-0.0217-0.26660.14450.10640.0461-0.0391-0.0918-0.3267-0.02440.1601-0.05660.05860.2084-0.11660.10730.4703-2.720310.9783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 6925 - 89
2X-RAY DIFFRACTION2AA70 - 8490 - 104
3X-RAY DIFFRACTION3AA85 - 109105 - 129
4X-RAY DIFFRACTION4AA110 - 207130 - 227
5X-RAY DIFFRACTION5AA208 - 241228 - 261
6X-RAY DIFFRACTION6AA242 - 265262 - 285
7X-RAY DIFFRACTION7AA266 - 283286 - 303
8X-RAY DIFFRACTION8AA284 - 313304 - 333
9X-RAY DIFFRACTION9AA314 - 327334 - 347
10X-RAY DIFFRACTION10AA328 - 436348 - 456
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top
X-RAY DIFFRACTION5ACO.paramACO.top

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