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- PDB-4nex: Structure of the N-acetyltransferase domain of X. fastidiosa NAGS/K -

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Basic information

Entry
Database: PDB / ID: 4nex
TitleStructure of the N-acetyltransferase domain of X. fastidiosa NAGS/K
ComponentsAcetylglutamate kinase
KeywordsTRANSFERASE / GCN5-related N-acetyltransferase dold / synthase
Function / homology
Function and homology information


acetylglutamate kinase / acetylglutamate kinase activity / arginine biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Acetylglutamate kinase ArgB, GNAT domain-containing / N-Acetyl-L-glutamate kinase, fungal-type / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain / NAT, N-acetyltransferase, of N-acetylglutamate synthase / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain profile. / Acetylglutamate kinase family / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Gcn5-related N-acetyltransferase (GNAT) ...Acetylglutamate kinase ArgB, GNAT domain-containing / N-Acetyl-L-glutamate kinase, fungal-type / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain / NAT, N-acetyltransferase, of N-acetylglutamate synthase / Vertebrate-like NAGS Gcn5-related N-acetyltransferase (GNAT) domain profile. / Acetylglutamate kinase family / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Gcn5-related N-acetyltransferase (GNAT) / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-ACETYL-L-GLUTAMATE / Acetylglutamate kinase
Similarity search - Component
Biological speciesXylella fastidiosa Temecula1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6955 Å
AuthorsZhao, G. / Jin, Z. / Allewell, N.M. / Tuchman, M. / Shi, D.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Structures of the N-acetyltransferase domain of Xylella fastidiosaN-acetyl-L-glutamate synthase/kinase with and without a His tag bound to N-acetyl-L-glutamate.
Authors: Zhao, G. / Jin, Z. / Allewell, N.M. / Tuchman, M. / Shi, D.
History
DepositionOct 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: 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

Downloads & links

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Assembly

Deposited unit
A: Acetylglutamate kinase
B: Acetylglutamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8077
Polymers39,1402
Non-polymers6675
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-64 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.718, 51.718, 242.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Acetylglutamate kinase / / N-acetyl-L-glutamate 5-phosphotransferase / NAG kinase / AGK


Mass: 19570.074 Da / Num. of mol.: 2 / Fragment: N-acetyltransferase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa Temecula1 (bacteria)
Strain: Temecula1 / ATCC 700964 / Gene: ArgA/B, argB, PD_0293 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q87EL2, acetylglutamate kinase
#2: Chemical ChemComp-NLG / N-ACETYL-L-GLUTAMATE / N-Acetylglutamic acid


Mass: 189.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO5
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / pH: 6.5
Details: 0.2 M Li2SO4, 0.1 M Tris, pH 6.5, 25% PEG3350 , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2013
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 13 % / Number: 485709 / Rmerge(I) obs: 0.079 / Χ2: 2.17 / D res high: 1.6955 Å / D res low: 50 Å / Num. obs: 37347 / % possible obs: 98.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.615091.110.0473.6258.8
3.664.6197.110.0534.13310.1
3.23.6699.310.064.23710.7
2.913.299.110.0734.0811.5
2.72.9199.510.0823.49112.8
2.542.799.610.0893.05513.5
2.412.5499.510.0992.75913.9
2.312.4199.410.1142.50914.2
2.222.3199.310.1292.31614.2
2.142.2299.210.142.06714.3
2.072.1499.210.1661.80814.4
2.022.079910.1941.56714.5
1.962.0299.110.2321.43514.5
1.911.9698.810.2921.27214.5
1.871.9198.910.3581.23814.5
1.831.8798.810.4261.15314.3
1.791.8398.710.4981.1213.8
1.761.7998.710.5241.05613
1.731.7698.110.6130.96612.1
1.71.7397.210.690.93710.9
ReflectionResolution: 1.6955→40 Å / Num. obs: 37347 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 55.8
Reflection shellResolution: 1.6955→1.73 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.4 / % possible all: 97.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S6H

3s6h


Resolution: 1.6955→39.33 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1866 5 %
Rwork0.189 --
obs0.191 37297 98.5 %
all-37857 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.28 Å2
Refinement stepCycle: LAST / Resolution: 1.6955→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 41 230 2795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072666
X-RAY DIFFRACTIONf_angle_d1.0993634
X-RAY DIFFRACTIONf_dihedral_angle_d14.031961
X-RAY DIFFRACTIONf_chiral_restr0.079375
X-RAY DIFFRACTIONf_plane_restr0.005469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6955-1.74130.32031380.26392606X-RAY DIFFRACTION96
1.7413-1.79260.28551400.24182667X-RAY DIFFRACTION99
1.7926-1.85040.30631410.22362673X-RAY DIFFRACTION99
1.8504-1.91660.24051410.21212683X-RAY DIFFRACTION99
1.9166-1.99330.25571420.20532698X-RAY DIFFRACTION99
1.9933-2.0840.24241420.20172684X-RAY DIFFRACTION99
2.084-2.19390.23861410.19132696X-RAY DIFFRACTION99
2.1939-2.33130.20791440.18782737X-RAY DIFFRACTION99
2.3313-2.51130.20991450.18592753X-RAY DIFFRACTION100
2.5113-2.7640.18771450.19132757X-RAY DIFFRACTION100
2.764-3.16380.20351470.18872794X-RAY DIFFRACTION100
3.1638-3.98540.19381500.17032850X-RAY DIFFRACTION99
3.9854-39.34360.22941500.1852833X-RAY DIFFRACTION93
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)
12.9677-0.76410.95991.9525-0.23261.63520.0387-0.05260.16580.0273-0.02580.0303-0.1285-0.0595-0.02130.1894-0.00490.03890.0962-0.00020.1628-9.16361.6169-26.957
22.7904-1.3298-1.21072.62630.75416.2249-0.0449-0.4631-0.27420.11760.2169-0.00640.97870.8026-0.15770.32020.0613-0.00530.32680.00280.250813.4572-9.2227-4.45
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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