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- PDB-5yge: ArgA complexed with AceCoA and glutamate -

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Basic information

Entry
Database: PDB / ID: 5yge
TitleArgA complexed with AceCoA and glutamate
ComponentsAmino-acid acetyltransferase
KeywordsTRANSFERASE / acetyltransferase / arginine biosynthesis / glutamate / acetyl coenzyme A
Function / homology
Function and homology information


acetyl-CoA:L-glutamate N-acetyltransferase activity / methione N-acyltransferase activity / amino-acid N-acetyltransferase / arginine biosynthetic process via ornithine / N-acetyltransferase activity / protein homotetramerization / protein homodimerization activity / cytoplasm
Similarity search - Function
Acetyltransferase NSI-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / CACODYLIC ACID / GLUTAMIC ACID / Amino-acid acetyltransferase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.039 Å
AuthorsYang, X. / Wu, L. / Ran, Y. / Xu, A. / Zhang, B. / Yang, X. / Zhang, R. / Rao, Z. / Li, J.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Crystal structure of l-glutamate N-acetyltransferase ArgA from Mycobacterium tuberculosis
Authors: Yang, X. / Wu, L. / Ran, Y. / Xu, A. / Zhang, B. / Yang, X. / Zhang, R. / Rao, Z. / Li, J.
History
DepositionSep 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amino-acid acetyltransferase
B: Amino-acid acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,62410
Polymers39,1592
Non-polymers2,4658
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-12 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.728, 73.728, 187.231
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-387-

HOH

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Components

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


Mass: 19579.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: argA, Rv2747 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O33289, amino-acid N-acetyltransferase
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE / Cacodylic acid


Mass: 137.997 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H7AsO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.35 Å3/Da / Density % sol: 63.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.08 M sodium cacodylate, pH6.2, 0.16 M magnesium acetate tetrahydrate, 12% (w/v) PEG10000, 20% (w/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97624 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.039→50 Å / Num. obs: 33893 / % possible obs: 99.9 % / Redundancy: 8.3 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.037 / Rrim(I) all: 0.109 / Χ2: 0.909 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.087.80.46316370.9210.1730.4960.93599.5
2.08-2.118.10.45816840.9360.1680.4890.89799.8
2.11-2.158.20.35616390.9630.130.380.868100
2.15-2.28.10.32316480.9690.1180.3440.84999.8
2.2-2.258.20.30616690.9710.1120.3260.916100
2.25-2.38.10.26716640.9740.0990.2851.045100
2.3-2.358.30.23716660.9810.0860.2520.852100
2.35-2.428.40.19616560.9840.0710.2090.858100
2.42-2.498.40.17816740.9880.0650.190.869100
2.49-2.578.50.16616710.9910.060.1770.839100
2.57-2.668.60.15716820.990.0560.1670.863100
2.66-2.778.60.13416790.9940.0480.1420.879100
2.77-2.898.80.11916900.9940.0420.1270.88699.9
2.89-3.058.80.116990.9950.0350.1070.87100
3.05-3.248.90.08816990.9960.0310.0930.886100
3.24-3.498.70.0817010.9950.0290.0850.99100
3.49-3.848.40.07517280.9960.0270.081.085100
3.84-4.3980.06817410.9970.0260.0731.072100
4.39-5.5480.06417660.9970.0240.0680.95399.8
5.54-507.70.05419000.9970.0210.0580.78599.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.039→36.17 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.11
RfactorNum. reflection% reflection
Rfree0.2209 1717 5.09 %
Rwork0.1968 --
obs0.1981 33763 99.77 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 22.352 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso max: 124.01 Å2 / Biso mean: 28.18 Å2 / Biso min: 6.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.1041 Å20 Å20 Å2
2--0.1041 Å2-0 Å2
3----0.2082 Å2
Refinement stepCycle: final / Resolution: 2.039→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 16 178 2847
Biso mean--62.24 33.14 -
Num. residues----340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012847
X-RAY DIFFRACTIONf_angle_d1.2413894
X-RAY DIFFRACTIONf_chiral_restr0.07442
X-RAY DIFFRACTIONf_plane_restr0.005480
X-RAY DIFFRACTIONf_dihedral_angle_d16.4121045
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0395-2.09950.29051540.24982565271998
2.0995-2.16720.28011400.21826262766100
2.1672-2.24470.24131160.216426222738100
2.2447-2.33460.30271460.219226182764100
2.3346-2.44080.22591410.204226382779100
2.4408-2.56940.22821360.213226422778100
2.5694-2.73040.26861510.215126492800100
2.7304-2.94110.25891270.220926902817100
2.9411-3.23690.22751440.215526752819100
3.2369-3.70490.20861540.192826852839100
3.7049-4.66620.15971670.155227312898100
4.6662-36.17530.19991410.1782905304699

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