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- PDB-4i49: Structure of ngNAGS bound with bisubstrate analog CoA-NAG -

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Basic information

Entry
Database: PDB / ID: 4i49
TitleStructure of ngNAGS bound with bisubstrate analog CoA-NAG
ComponentsAmino-acid acetyltransferase
KeywordsTRANSFERASE / Protein-bisubstrate analog complex / Synthase
Function / homology
Function and homology information


amino-acid N-acetyltransferase
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
Chem-1C4 / Amino-acid acetyltransferase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae SK-93-1035 (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.75 Å
AuthorsShi, D. / Zhao, G. / Allewell, N.M. / Tuchman, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Structure of the complex of Neisseria gonorrhoeae N-acetyl-l-glutamate synthase with a bound bisubstrate analog.
Authors: Zhao, G. / Allewell, N.M. / Tuchman, M. / Shi, D.
History
DepositionNov 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 20, 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

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Assembly

Deposited unit
A: Amino-acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2863
Polymers49,2351
Non-polymers1,0512
Water61334
1
A: Amino-acid acetyltransferase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)301,71718
Polymers295,4136
Non-polymers6,30412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_554-y,-x,-z-11
crystal symmetry operation5_554-x+y,y,-z-11
crystal symmetry operation6_554x,x-y,-z-11
Buried area22380 Å2
ΔGint-191 kcal/mol
Surface area103610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.521, 98.521, 90.009
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312

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Components

#1: Protein Amino-acid acetyltransferase / N-acetylglutamate synthase


Mass: 49235.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae SK-93-1035 (bacteria)
Strain: ATCC53420 / Gene: argA, NGLG_00316 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D1ED56, amino-acid N-acetyltransferase
#2: Chemical ChemComp-1C4 / (2S)-2-({(3S,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14,20-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaicosan-20-yl}amino)pentanedioic acid (non-preferred name)


Mass: 954.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H45N8O21P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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, sitting drop / pH: 5.6
Details: 100 mM Tri-Na citrate, 0.2M MgCl2, 8% PEG3350 , pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 20, 2011
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 13177 / Num. obs: 13151 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 53.39 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.9
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 1.55 / Num. unique all: 647 / % possible all: 64.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3B8G

3b8g


Resolution: 2.75→24.042 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7922 / SU ML: 0.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 27.67 / Stereochemistry target values: ML / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2713 1331 10.12 %RANDOM
Rwork0.1893 ---
obs0.1977 13149 99.93 %-
all-13151 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.45 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 118.41 Å2 / Biso mean: 49.4288 Å2 / Biso min: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.8429 Å20 Å2-0 Å2
2--0.8429 Å20 Å2
3----1.6859 Å2
Refinement stepCycle: LAST / Resolution: 2.75→24.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 66 34 3327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083347
X-RAY DIFFRACTIONf_angle_d1.1884533
X-RAY DIFFRACTIONf_chiral_restr0.074508
X-RAY DIFFRACTIONf_plane_restr0.004592
X-RAY DIFFRACTIONf_dihedral_angle_d18.4341226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7503-2.84840.37431340.287611701304100
2.8484-2.96230.36331340.269411791313100
2.9623-3.09680.33561330.231911691302100
3.0968-3.25970.34481270.220111701297100
3.2597-3.46340.29071290.216511651294100
3.4634-3.72990.28831320.195311861318100
3.7299-4.10360.26791280.176511891317100
4.1036-4.69360.2221380.143611801318100
4.6936-5.89890.22521310.172311831314100
5.8989-24.04310.24511450.16891227137299

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