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- PDB-3d2m: Crystal structure of N-acetylglutamate synthase from Neisseria go... -

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Basic information

Entry
Database: PDB / ID: 3d2m
TitleCrystal structure of N-acetylglutamate synthase from Neisseria gonorrhoeae complexed with coenzyme A and L-glutamate
ComponentsPutative acetylglutamate synthase
KeywordsTRANSFERASE / Protein-CoA-Glu ternary 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
COENZYME A / GLUTAMIC ACID / Amino-acid acetyltransferase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsShi, D. / Min, L. / Jin, Z. / Allewell, N.M. / Tuchman, M.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Mechanism of Allosteric Inhibition of N-Acetyl-L-glutamate Synthase by L-Arginine.
Authors: Min, L. / Jin, Z. / Caldovic, L. / Morizono, H. / Allewell, N.M. / Tuchman, M. / Shi, D.
History
DepositionMay 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)50,1503
Polymers49,2351
Non-polymers9152
Water1,45981
1
A: Putative acetylglutamate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)300,90118
Polymers295,4136
Non-polymers5,48812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation4_666-y+1,-x+1,-z+11
crystal symmetry operation5_656-x+y+1,y,-z+11
crystal symmetry operation6_556x,x-y,-z+11
Buried area27670 Å2
ΔGint-60.8 kcal/mol
Surface area104070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.802, 98.802, 90.107
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312

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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: ATCC53420 / Gene: argA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5FAK7, amino-acid N-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 52.3 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.4
Details: 8% PEG3350, 100 mM ammonium citrate, pH 6.4, EVAPORATION, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 19, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→90.17 Å / Num. all: 25434 / Num. obs: 24544 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 37.5
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 1.3 / Num. unique all: 1836 / % possible all: 72.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CBASSdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3B8G

3b8g


Resolution: 2.21→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.925 / SU B: 17.267 / SU ML: 0.218 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.304 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2803 1247 5.1 %RANDOM
Rwork0.22856 ---
obs0.23108 23293 96.69 %-
all-24090 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.19 Å20 Å2
2---0.38 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 58 81 3366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213339
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9744521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0775422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23822.81153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72715543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4931534
X-RAY DIFFRACTIONr_chiral_restr0.1170.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022535
X-RAY DIFFRACTIONr_nbd_refined0.2440.21505
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22236
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.27
X-RAY DIFFRACTIONr_mcbond_it0.891.52153
X-RAY DIFFRACTIONr_mcangle_it1.46923320
X-RAY DIFFRACTIONr_scbond_it2.44631327
X-RAY DIFFRACTIONr_scangle_it3.7884.51201
LS refinement shellResolution: 2.21→2.268 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 60 -
Rwork0.314 1296 -
obs-1836 72.13 %
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)
12.27540.20690.42393.00050.18880.33910.1230.09440.0316-0.0211-0.10510.55550.0279-0.0619-0.01790.12140.0287-0.05270.12180.07590.13719.173324.15139.7765
25.30816.36792.72697.63933.27131.4009-0.5072-0.20592.94580.28490.34340.3218-0.6373-1.05670.16380.45680.3443-0.27750.06250.48861.02345.938148.303428.878
33.24870.048-0.88836.7549-5.42018.82910.2034-0.13790.71620.0806-0.18780.98930.07170.1124-0.0156-0.0804-0.0158-0.0338-0.04850.02430.375316.475242.298342.3417
41.0841-0.29311.01572.1801-0.47281.5435-0.07670.25050.4939-0.4349-0.01150.2966-0.34150.12720.08820.14110.0042-0.0911-0.00190.15250.096126.162442.142431.5194
54.1813-1.682-1.76591.5590.70552.57010.0210.8136-0.6621-0.3253-0.2620.69370.264-0.40430.2410.06670.0465-0.20550.1635-0.02460.092313.106922.557823.7783
61.84990.3641-0.16320.8645-1.57653.02290.22680.4241-0.1634-0.0447-0.05440.1682-0.1757-0.086-0.17240.17180.1269-0.13090.13570.0250.056715.465326.841624.2343
77.9171-0.4685-1.73757.1169-5.69895.248-0.24250.4257-0.4591-0.63860.13080.12950.8904-0.63120.11170.25820.0361-0.19450.0544-0.09230.077918.508917.004927.7452
84.2906-3.03651.77794.7458-2.56315.8289-0.27460.19220.0704-0.60180.0478-0.6468-0.44490.26510.22680.2089-0.22620.21360.0698-0.18830.069437.77714.52410.4906
91.9183-0.30210.0974.6842-0.9651.9823-0.001-0.40310.1554-0.20750.2699-0.2447-0.0803-0.2461-0.26880.0966-0.14010.11190.2397-0.2136-0.021529.939-3.696711.3535
1016.0847-10.2876-4.983414.14943.38289.7594-0.1252-0.3213-0.7618-0.00370.0510.54050.2184-0.850.07430.0288-0.35240.13190.2282-0.23720.057529.5908-9.872913.9675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 6825 - 88
2X-RAY DIFFRACTION2AA69 - 8489 - 104
3X-RAY DIFFRACTION3AA85 - 124105 - 144
4X-RAY DIFFRACTION4AA125 - 199145 - 219
5X-RAY DIFFRACTION5AA200 - 227220 - 247
6X-RAY DIFFRACTION6AA228 - 269248 - 289
7X-RAY DIFFRACTION7AA270 - 285290 - 305
8X-RAY DIFFRACTION8AA286 - 339306 - 359
9X-RAY DIFFRACTION9AA340 - 420360 - 440
10X-RAY DIFFRACTION10AA421 - 436441 - 456

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