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- PDB-2r98: Crystal Structure of N-acetylglutamate synthase (selenoMet substi... -

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Basic information

Entry
Database: PDB / ID: 2r98
TitleCrystal Structure of N-acetylglutamate synthase (selenoMet substituted) from Neisseria gonorrhoeae
ComponentsPutative acetylglutamate synthase
KeywordsTRANSFERASE / Protein-AcCoA complex
Function / homology
Function and homology information


L-glutamate N-acetyltransferase activity / L-methionine N-acyltransferase activity / amino-acid N-acetyltransferase / L-arginine biosynthetic process / cytoplasm
Similarity search - Function
N-acetylglutamate synthase, kinase-like domain / Amino-acid N-acetyltransferase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. ...N-acetylglutamate synthase, kinase-like domain / Amino-acid N-acetyltransferase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 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: 2.4 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 12, 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 / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
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 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)50,3262
Polymers49,5171
Non-polymers8101
Water1,65792
1
A: Putative acetylglutamate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)301,95912
Polymers297,1016
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 area28090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.975, 98.975, 89.292
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-476-

HOH

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Components

#1: Protein Putative acetylglutamate synthase


Mass: 49516.859 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


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


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 6% PEG3350, 100mM CsCl, 100 mM sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97472 Å
DetectorDetector: CCD / Date: Jun 18, 2007
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97472 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 19726 / Num. obs: 19707 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 33.8
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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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: 2.4→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.787 / SU ML: 0.216 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. For this and related entry 2R8V, 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 2R8V, 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
Rfree0.24394 1010 5.1 %RANDOM
Rwork0.19437 ---
obs0.19694 18665 99.52 %-
all-19707 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.527 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.63 Å20 Å2
2--1.25 Å20 Å2
3----1.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 51 92 3370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9744514
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7035422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02222.763152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.4615541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4111534
X-RAY DIFFRACTIONr_chiral_restr0.1980.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.022530
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2930.31534
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.52204
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.5169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.376
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5311.52137
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.67423316
X-RAY DIFFRACTIONr_scbond_it6.42331315
X-RAY DIFFRACTIONr_scangle_it8.9424.51198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 73 -
Rwork0.271 1360 -
obs--97.68 %
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)
11.81060.4082-0.09452.8542-0.44950.81880.05290.07660.01120.14340.01180.44710.0462-0.0778-0.06470.1235-0.0141-0.06420.13340.04730.130819.040824.253739.4259
21.22353.35713.25799.21158.9398.6747-0.5499-1.53821.0344-2.24990.05621.0586-1.5022.06520.49370.5566-0.097-0.28930.54130.44290.65135.626748.374528.9203
32.5527-0.7335-0.53355.8361-4.27396.5064-0.0171-0.13640.49190.02430.04250.41490.2054-0.0791-0.0254-0.00090.007-0.03210.07180.0080.253516.67742.224542.127
41.55970.0030.43732.0961-0.26550.9269-0.01630.30760.2496-0.3119-0.0310.243-0.07830.04870.04740.13810.011-0.06470.10070.07680.111323.290638.667129.951
510.90412.65422.06290.72680.64094.63640.22350.4882-0.0382-0.1659-0.22060.06160.02910.0824-0.00290.12460.0892-0.07220.1563-0.0114-0.02816.075726.556919.0574
61.4975-1.8549-0.98792.35830.78083.8882-0.14550.2688-0.38860.05790.07430.41220.5414-0.32720.07120.1165-0.0067-0.0970.15650.01360.133315.176419.251432.2353
74.7342-1.35311.24186.687-1.55956.6237-0.41270.24740.2058-0.91330.3701-0.7704-0.41330.3290.04260.2487-0.32440.18980.0482-0.14190.052638.99484.51592.8526
85.03266.55151.346111.9304-1.00242.5909-0.60680.3947-0.2339-1.05880.661-0.9863-0.31710.5125-0.05420.3055-0.25070.17020.1286-0.12110.009334.12442.75440.0273
92.60141.19851.6483.5630.45992.8059-0.1009-0.21390.1568-0.17640.15780.0196-0.4067-0.0958-0.05690.1541-0.08660.11460.1207-0.1090.029629.94060.73510.8527
102.6601-0.20450.34487.57923.24685.850.0245-0.2733-0.1262-0.0840.295-0.14520.1357-0.3671-0.31960.1356-0.15330.05290.2331-0.05440.016730.2583-10.30814.0813
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 - 125105 - 145
4X-RAY DIFFRACTION4AA126 - 217146 - 237
5X-RAY DIFFRACTION5AA218 - 256238 - 276
6X-RAY DIFFRACTION6AA257 - 283277 - 303
7X-RAY DIFFRACTION7AA284 - 316304 - 336
8X-RAY DIFFRACTION8AA317 - 347337 - 367
9X-RAY DIFFRACTION9AA348 - 396368 - 416
10X-RAY DIFFRACTION10AA397 - 436417 - 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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