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- PDB-3dr8: Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella t... -

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Basic information

Entry
Database: PDB / ID: 3dr8
TitleStructure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium with its cofactor Acetyl-CoA
ComponentsyncA
KeywordsTRANSFERASE / Salmonella essential gene IDP0086 acetyltransferase cofactor acetyl-CoA / TRANSFERASE. FUNDED BY THE NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES OF NIH CONTRACT NUMBER HHSN272200700058C / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
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
ACETYL COENZYME *A / ACETATE ION / L-methionine sulfoximine/L-methionine sulfone acetyltransferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSinger, A.U. / Skarina, T. / Onopriyenko, O. / Edwards, A.M. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Structure of yncA, a putative ACETYLTRANSFERASE from Salmonella typhimurium with its cofactor Acetyl-CoA
Authors: Singer, A.U. / Skarina, T. / Onopriyenko, O. / Edwards, A.M. / Anderson, W.F. / Savchenko, A.
History
DepositionJul 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: yncA
B: yncA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,40313
Polymers39,3472
Non-polymers2,05611
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-40 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.254, 71.374, 74.005
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 yncA


Mass: 19673.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SNA at N-terminus following cleavage of His-tag with TEV protease
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: yncA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3)
References: UniProt: Q8ZPD3*PLUS, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 295 K / pH: 5.6
Details: 1.4 M Sodium Acetate trihydrate 5.6 pH plus 5 mM Acetyl Coenzyme A, cryoprotected with N-paratone oil, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 30, 2008 / Details: Osmic mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. all: 28962 / Num. obs: 28378 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 21
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 5.3 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: molecule A of 2BL1

2bl1


Resolution: 1.95→47.35 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.279 / SU ML: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.216 1255 5.1 %
Rwork0.154 --
obs0.157 24632 98.3 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 20.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 126 387 3246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212995
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9614064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0715357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.922.797143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16915450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8081525
X-RAY DIFFRACTIONr_chiral_restr0.1110.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022299
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21470
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22018
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2336
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8611.51817
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35922823
X-RAY DIFFRACTIONr_scbond_it2.5231345
X-RAY DIFFRACTIONr_scangle_it3.5314.51240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å
RfactorNum. reflection% reflection
Rfree0.273 85 -
Rwork0.173 1655 -
obs--96.72 %

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