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- PDB-4nxy: Crystal Structure of the GNAT domain of S. lividans PAT -

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Basic information

Entry
Database: PDB / ID: 4nxy
TitleCrystal Structure of the GNAT domain of S. lividans PAT
ComponentsAcyl-CoA synthetase
KeywordsTRANSFERASE / Lysine Acetyltransferase / AMP-Forming Acetate:CoA Ligase Enzyme (Acs)
Function / homology
Function and homology information


N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Succinyl-CoA synthetase-like, flavodoxin domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain ...Succinyl-CoA synthetase-like, flavodoxin domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIFLUOROETHANOL / Acyl-CoA synthetase / Acyl-CoA synthetase
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.449 Å
AuthorsRank, K.C. / Tucker, A.C. / Escalante-Semerena, J.C. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Insights into the specificity of lysine acetyltransferases.
Authors: Tucker, A.C. / Taylor, K.C. / Rank, K.C. / Rayment, I. / Escalante-Semerena, J.C.
History
DepositionDec 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Acyl-CoA synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8453
Polymers21,6531
Non-polymers1922
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.056, 56.711, 74.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Acyl-CoA synthetase


Mass: 21653.266 Da / Num. of mol.: 1 / Fragment: GNAT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Strain: TK24 / Gene: SSPG_01886 / Production host: Escherichia coli (E. coli) / References: UniProt: D6EP29, UniProt: A0A7U8YS53*PLUS
#2: Chemical ChemComp-ETF / TRIFLUOROETHANOL


Mass: 100.040 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3F3O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.94 Å3/Da / Density % sol: 36.62 %
Crystal growTemperature: 298 K / Method: batch / pH: 7
Details: 22% monomethyl polyethylene glycol 5000, 100 mM MOPS pH 7.0, 25 mM MgCl2, 2% 2,2,2-trifluoroethanol, 6% glycerol, Batch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97936 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 4, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 1.449→25 Å / Num. all: 30626 / Num. obs: 30540 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 58.854
Reflection shellResolution: 1.449→1.48 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 10.07 / Num. unique all: 1475 / Rsym value: 0.212 / % possible all: 98.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.449→24.52 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.208 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21678 1540 5 %RANDOM
Rwork0.17649 ---
all0.17845 29002 --
obs0.17845 29002 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.384 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.449→24.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 12 185 1586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0191459
X-RAY DIFFRACTIONr_bond_other_d0.0010.021372
X-RAY DIFFRACTIONr_angle_refined_deg2.4411.9481984
X-RAY DIFFRACTIONr_angle_other_deg1.00133133
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28522.10576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16115223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5191517
X-RAY DIFFRACTIONr_chiral_restr0.1380.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02369
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.449→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 119 -
Rwork0.218 2047 -
obs--97.26 %

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