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- PDB-5ix3: Crystal structure of N-acetyltransferase from Staphylococcus aureus. -

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Basic information

Entry
Database: PDB / ID: 5ix3
TitleCrystal structure of N-acetyltransferase from Staphylococcus aureus.
ComponentsDiamine N-acetyltransferase
KeywordsTRANSFERASE / N-acetyltransferase / GNATs / SPEG / Staphylococcus aureus
Function / homology
Function and homology information


diamine N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
Diamine N-acetyltransferase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsSrivastava, P. / Khandokar, Y. / Forwood, J.
CitationJournal: To Be Published
Title: Crystal structure of N-acetyltransferase from Staphylococcus aureus.
Authors: Srivastava, P. / Khandokar, Y. / Forwood, J.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Other
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diamine N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)20,0791
Polymers20,0791
Non-polymers00
Water1,982110
1
A: Diamine N-acetyltransferase
x 12


Theoretical massNumber of molelcules
Total (without water)240,94712
Polymers240,94712
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_345-y-2,x-y-1,z1
crystal symmetry operation3_435-x+y-1,-x-2,z1
crystal symmetry operation4_335-x-2,-y-2,z1
crystal symmetry operation5_545y,-x+y-1,z1
crystal symmetry operation6_455x-y-1,x,z1
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation8_437x-y-1,-y-2,-z+21
crystal symmetry operation9_347-x-2,-x+y-1,-z+21
crystal symmetry operation10_337-y-2,-x-2,-z+21
crystal symmetry operation11_457-x+y-1,y,-z+21
crystal symmetry operation12_547x,x-y-1,-z+21
Buried area32360 Å2
ΔGint-103 kcal/mol
Surface area83180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.950, 107.950, 65.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-211-

HOH

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Components

#1: Protein Diamine N-acetyltransferase / Spermidine N(1)-acetyltransferase / Spermidine acetyltransferase


Mass: 20078.924 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: res, speG, AL498_11440, ERS092844_02726, ERS195423_02759, R114_33, R92_33
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U5NVV0, diamine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8 / Details: 0.1M NaCl, 0.1M HEPES pH8.0, 1.6M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2015
RadiationMonochromator: silicon double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.81→38 Å / Num. obs: 20350 / % possible obs: 97.4 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 13.19
Reflection shellResolution: 1.81→1.87 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.29 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→37 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.389 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24731 1010 5 %RANDOM
Rwork0.22171 ---
obs0.223 19309 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.166 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0.26 Å2-0 Å2
2---0.53 Å2-0 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 1.81→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 0 110 1514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191447
X-RAY DIFFRACTIONr_bond_other_d0.0030.021372
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9571948
X-RAY DIFFRACTIONr_angle_other_deg1.04933164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.965167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.50124.54577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33715272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.892155
X-RAY DIFFRACTIONr_chiral_restr0.1260.2205
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021608
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02349
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_it2.9752.86665
X-RAY DIFFRACTIONr_mcbond_other2.9622.855664
X-RAY DIFFRACTIONr_mcangle_it3.8644.263830
X-RAY DIFFRACTIONr_mcangle_other3.8684.268831
X-RAY DIFFRACTIONr_scbond_it4.5213.479782
X-RAY DIFFRACTIONr_scbond_other4.5193.482783
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8465.0031117
X-RAY DIFFRACTIONr_long_range_B_refined8.63828.5676130
X-RAY DIFFRACTIONr_long_range_B_other8.58928.4256056
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 73 -
Rwork0.298 1364 -
obs--94.79 %

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