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- PDB-5jph: Structure of a GNAT acetyltransferase SACOL1063 from Staphylococc... -

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Basic information

Entry
Database: PDB / ID: 5jph
TitleStructure of a GNAT acetyltransferase SACOL1063 from Staphylococcus aureus in complex with CoA
ComponentsAcetyltransferase SACOL1063
KeywordsTRANSFERASE / acetyltransferase / Gcn5-related N-acetyltransferase / GNAT / protein acetylation / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


glucosamine 6-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase (GNAT) domain / Glucosamine 6-phosphate N-acetyltransferase / 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
COENZYME A / Acetyltransferase SACOL1063
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.46 Å
AuthorsMajorek, K.A. / Osinski, T. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Insight into the 3D structure and substrate specificity of previously uncharacterized GNAT superfamily acetyltransferases from pathogenic bacteria.
Authors: Majorek, K.A. / Osinski, T. / Tran, D.T. / Revilla, A. / Anderson, W.F. / Minor, W. / Kuhn, M.L.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Other
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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: Acetyltransferase SACOL1063
B: Acetyltransferase SACOL1063
C: Acetyltransferase SACOL1063
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,62512
Polymers50,9133
Non-polymers4,7129
Water11,638646
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-28 kcal/mol
Surface area20610 Å2
2
A: Acetyltransferase SACOL1063
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5424
Polymers16,9711
Non-polymers1,5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-7 kcal/mol
Surface area7410 Å2
MethodPISA
3
B: Acetyltransferase SACOL1063
hetero molecules

C: Acetyltransferase SACOL1063
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0838
Polymers33,9422
Non-polymers3,1416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y+1/2,-z+31
Buried area5500 Å2
ΔGint-22 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.088, 93.821, 68.910
Angle α, β, γ (deg.)90.000, 97.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A0 - 140
2010B0 - 140
1020A0 - 140
2020C0 - 140
1030B-2 - 141
2030C-2 - 141

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Acetyltransferase SACOL1063 / GCN5-related N-acetyltransferase / GNAT


Mass: 16970.990 Da / Num. of mol.: 3 / Mutation: V28I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: SACOL1063 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5HH30, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-tris propane pH 7.0 and 2.2 M DL-Malic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2013 / Details: mirrors
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 108551 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/av σ(I): 36.747 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.46-1.494.60.6722.1198.3
1.49-1.514.80.547198.4
1.51-1.544.80.458198.6
1.54-1.574.80.369198.9
1.57-1.614.80.332198.8
1.61-1.644.80.29198.7
1.64-1.694.80.238199.1
1.69-1.734.80.203199.2
1.73-1.784.80.162199.2
1.78-1.844.80.135199.2
1.84-1.914.80.116199.6
1.91-1.984.80.096199.6
1.98-2.074.80.08199.7
2.07-2.184.80.069199.8
2.18-2.324.80.067199.9
2.32-2.54.80.065199.9
2.5-2.754.70.0641100
2.75-3.154.70.0571100
3.15-3.964.60.039199.8
3.96-504.50.041194.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.46→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.738 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0565 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.054
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1697 5418 5 %RANDOM
Rwork0.1417 ---
obs0.1431 102969 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.2 Å2 / Biso mean: 22.71 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.29 Å2
2--0.29 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.46→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 291 647 4370
Biso mean--28.79 36.26 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194148
X-RAY DIFFRACTIONr_bond_other_d0.0050.023869
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9845651
X-RAY DIFFRACTIONr_angle_other_deg1.77138968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23524.785186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90115664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3961524
X-RAY DIFFRACTIONr_chiral_restr0.0980.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024991
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02921
X-RAY DIFFRACTIONr_mcbond_it1.7362.2681900
X-RAY DIFFRACTIONr_mcbond_other1.7492.1741899
X-RAY DIFFRACTIONr_mcangle_it2.1662421
X-RAY DIFFRACTIONr_rigid_bond_restr8.64233813
X-RAY DIFFRACTIONr_sphericity_bonded11.23153725
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A178380.08
12B178380.08
21A174680.1
22C174680.1
31B175500.1
32C175500.1
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 388 -
Rwork0.231 7545 -
all-7933 -
obs--98.41 %

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