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- PDB-4u5y: Crystal Structure of the complex between the GNAT domain of S. li... -

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Basic information

Entry
Database: PDB / ID: 4u5y
TitleCrystal Structure of the complex between the GNAT domain of S. lividans PAT and the acetyl-CoA synthetase C-terminal domain of S. enterica
Components
  • Acetyl-coenzyme A synthetase
  • Acyl-CoA synthetase
KeywordsLIGASE / GNAT / COMPLEX / ACETYLATION / PAT
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 / ANL, C-terminal domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / GMP Synthetase; Chain A, domain 3 ...Succinyl-CoA synthetase-like, flavodoxin domain / Succinyl-CoA ligase like flavodoxin domain / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ANL, C-terminal domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / GMP Synthetase; Chain A, domain 3 / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / NAD(P)-binding domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Acyl-CoA synthetase / Acyl-CoA synthetase / :
Similarity search - Component
Biological speciesStreptomyces lividans TK24 (bacteria)
Salmonella enterica subsp. enterica serovar Paratyphi B str. ATCC 10719 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.926 Å
AuthorsTaylor, K.C. / Tucker, A.C. / Rank, K.C. / Escalante-Semerena, J.C. / Rayment, I.
Funding support United States, 2items
OrganizationGrant numberCountry
USPHSGM062203 United States
USPHSGM083987 United States
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
DepositionJul 25, 2014Deposition 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 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list / refine_hist
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA synthetase
D: Acetyl-coenzyme A synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3974
Polymers36,2052
Non-polymers1922
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-37 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.478, 66.524, 138.539
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

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Components

#1: Protein Acyl-CoA synthetase


Mass: 21669.332 Da / Num. of mol.: 1 / Fragment: UNP residues 1-194 / Mutation: S73C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans TK24 (bacteria) / Gene: SSPG_01886 / Production host: Escherichia coli (E. coli) / References: UniProt: D6EP29, UniProt: A0A7U8YS53*PLUS
#2: Protein Acetyl-coenzyme A synthetase / Acs / Acetate--CoA ligase / Acyl-activating enzyme


Mass: 14535.637 Da / Num. of mol.: 1 / Fragment: UNP residues 518-652 / Mutation: H567C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Paratyphi B str. ATCC 10719 (bacteria)
Gene: acs, SEEPB719_19728 / Production host: Escherichia coli (E. coli) / References: UniProt: V1Q8H8, acetate-CoA ligase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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: 1.99 Å3/Da / Density % sol: 38.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 11.2% (w/v) polyethylene glycol 8000, 100 mM 1,4-piperazinediethanesulfonic acid pH 6.5, 120 mM Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 14, 2014
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator: Water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22055 / % possible obs: 99.7 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.067 / Net I/av σ(I): 30.5 / Net I/σ(I): 24.3
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.9 / % possible all: 98.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NXY, 1PG4

4nxy

1pg4


Resolution: 1.926→21.632 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 1035 4.69 %Random Selection
Rwork0.1868 ---
obs0.1893 22055 99.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.8 Å2
Refinement stepCycle: LAST / Resolution: 1.926→21.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 10 185 2396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082254
X-RAY DIFFRACTIONf_angle_d1.0443055
X-RAY DIFFRACTIONf_dihedral_angle_d12.487825
X-RAY DIFFRACTIONf_chiral_restr0.044338
X-RAY DIFFRACTIONf_plane_restr0.005398
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
1.9264-2.02790.28191554.690.2005281195
2.0279-2.15480.24661330.18532997100
2.1548-2.3210.23031330.18873017100
2.321-2.55430.24221580.20262997100
2.5543-2.92310.23091430.20573006100
2.9231-3.67990.23971510.18343058100
3.6799-21.63340.23271620.1716313499

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