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- PDB-3b8g: Crysta structure of N-acetylglutamate synthase from Neisseria gon... -

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Basic information

Entry
Database: PDB / ID: 3b8g
TitleCrysta structure of N-acetylglutamate synthase from Neisseria gonorrhoeae complexed with coenzyme A and N-acetyl-glutamate
ComponentsPutative acetylglutamate synthase
KeywordsTRANSFERASE / Protein-CoA-NAG ternary complex
Function / homology
Function and homology information


methione N-acyltransferase activity / amino-acid N-acetyltransferase / acetyl-CoA:L-glutamate N-acetyltransferase activity / 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 / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 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 / 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 / N-ACETYL-L-GLUTAMATE / Amino-acid acetyltransferase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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
DepositionNov 1, 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 1.4Aug 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)50,1923
Polymers49,2351
Non-polymers9572
Water2,288127
1
A: Putative acetylglutamate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)301,15318
Polymers295,4136
Non-polymers5,74012
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 area27400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.650, 98.650, 89.754
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-472-

HOH

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Components

#1: Protein Putative acetylglutamate synthase


Mass: 49235.492 Da / Num. of mol.: 1 / Mutation: V312I, D336N and P427S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: ATCC53420 / 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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-NLG / N-ACETYL-L-GLUTAMATE


Mass: 189.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 51.96 %
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 25, 2007 / Details: mirrors
RadiationMonochromator: YALE MIrrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 15619 / Num. obs: 15494 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.927 / Mean I/σ(I) obs: 1.5 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
CNS1.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R8V

2r8v


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 26.874 / SU ML: 0.289 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.967 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28239 773 5 %RANDOM
Rwork0.19998 ---
obs0.20392 14685 98.91 %-
all-15494 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----0.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 61 127 3415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213342
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4071.9774525
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5545422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.4722.763152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.06915541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8031534
X-RAY DIFFRACTIONr_chiral_restr0.1630.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.022540
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3170.31789
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.350.52281
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.5245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3510.390
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3160.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5451.52131
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.98623320
X-RAY DIFFRACTIONr_scbond_it6.86231326
X-RAY DIFFRACTIONr_scangle_it9.8484.51205
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.596→2.663 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 57 -
Rwork0.381 1042 -
obs--95.57 %
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)
110.61661.5136-11.0660.2158-1.577711.5344-0.57830.6951-0.2904-0.31130.5401-0.04790.4732-1.10560.03820.0962-0.0731-0.10590.14260.03980.215419.6816.758541.9244
23.7128-0.5840.70163.177-0.40091.65160.1198-0.11730.00120.0158-0.03750.38110.0937-0.076-0.08230.1803-0.0241-0.03120.13850.04370.158518.795328.957338.9691
314.55328.4833-1.96047.5569-0.5570.3954-0.3630.46851.4993-0.3331-0.37570.62750.6183-1.72580.73870.15110.1219-0.1564-0.00290.2750.51665.264748.281229.1165
42.01470.5995-0.55124.3819-2.92943.80490.07080.11290.3094-0.08180.21950.5247-0.02250.1235-0.29030.09890.0069-0.04490.08150.06250.280115.267944.347840.1553
52.1143-1.56892.14633.1991-3.92216.55690.18240.05870.2049-0.29530.05680.50270.3102-0.0124-0.23920.14090.0079-0.03230.03630.05190.215822.061645.004431.2423
61.5876-0.22410.20221.32640.13791.4750.13010.28410.0337-0.1611-0.11320.08120.0099-0.0588-0.01690.1410.0243-0.05170.14220.04630.112121.366933.01528.185
73.2649-0.851-4.07973.4332-1.27917.15080.41310.04280.0454-0.2307-0.12370.3033-0.12720.1277-0.28940.18790.0446-0.12940.1726-0.03310.150917.193527.310625.4662
81.2591-1.4789-2.64513.21313.76635.85130.06260.07240.0178-0.2950.0546-0.1456-0.4018-0.2792-0.11710.0861-0.0509-0.0670.1441-0.01880.092826.270613.453315.0213
90.8410.58231.40152.4438-0.97024.1808-0.19660.40870.2021-0.33830.1541-0.3714-0.15730.34630.04250.1728-0.08240.14910.074-0.12090.147537.22721.15021.3912
102.00150.25720.82313.93210.20552.43560.0834-0.37860.09810.08130.05860.00010.0599-0.318-0.1420.1368-0.06460.08480.2468-0.10570.070329.9568-4.698912.4817
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1725 - 37
2X-RAY DIFFRACTION2AA18 - 6838 - 88
3X-RAY DIFFRACTION3AA69 - 8389 - 103
4X-RAY DIFFRACTION4AA84 - 111104 - 131
5X-RAY DIFFRACTION5AA112 - 148132 - 168
6X-RAY DIFFRACTION6AA149 - 236169 - 256
7X-RAY DIFFRACTION7AA237 - 266257 - 286
8X-RAY DIFFRACTION8AA267 - 303287 - 323
9X-RAY DIFFRACTION9AA304 - 347324 - 367
10X-RAY DIFFRACTION10AA348 - 436368 - 456
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2nlg.paramnlg.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5COA.paramCOA.top

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