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- PDB-8fv1: SpeG spermidine N-acetyltransferase from Staphylococcus aureus in... -

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Basic information

Entry
Database: PDB / ID: 8fv1
TitleSpeG spermidine N-acetyltransferase from Staphylococcus aureus in complex with spermine
ComponentsDiamine N-acetyltransferase
KeywordsTRANSFERASE
Function / homologyAcetyltransferase (GNAT) domain / diamine N-acetyltransferase / diamine N-acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / SPERMINE / Diamine N-acetyltransferase
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsTsimbalyuk, S. / Forwood, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: SpeG spermidine N-acetyltransferase from Staphylococcus aureus in complex with spermine, crystal form II
Authors: Tsimbalyuk, S. / Forwood, J.K.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 8, 2023ID: 7KY4
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Diamine N-acetyltransferase
A: Diamine N-acetyltransferase
B: Diamine N-acetyltransferase
D: Diamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1218
Polymers80,3124
Non-polymers8094
Water00
1
C: Diamine N-acetyltransferase
A: Diamine N-acetyltransferase
B: Diamine N-acetyltransferase
D: Diamine N-acetyltransferase
hetero molecules

C: Diamine N-acetyltransferase
A: Diamine N-acetyltransferase
B: Diamine N-acetyltransferase
D: Diamine N-acetyltransferase
hetero molecules

C: Diamine N-acetyltransferase
A: Diamine N-acetyltransferase
B: Diamine N-acetyltransferase
D: Diamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,36324
Polymers240,93512
Non-polymers2,42812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)161.683, 161.683, 161.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

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Components

#1: Protein
Diamine N-acetyltransferase


Mass: 20077.939 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: res / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U5NVV0
#2: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H26N4
Has ligand of interestN

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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: 4.36 Å3/Da / Density % sol: 71.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1M NaCl, 0.1M HEPES pH8.0, 1.6M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.95→24.95 Å / Num. obs: 29846 / % possible obs: 99.75 % / Redundancy: 20 % / Biso Wilson estimate: 77.58 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.9
Reflection shellResolution: 2.95→3.13 Å / Num. unique obs: 2792 / CC1/2: 0.681

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ix3

5ix3


Resolution: 2.95→24.95 Å / SU ML: 0.4095 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2475 1440 4.83 %
Rwork0.2289 28395 -
obs0.2299 29835 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.41 Å2
Refinement stepCycle: LAST / Resolution: 2.95→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 56 0 5628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00165756
X-RAY DIFFRACTIONf_angle_d0.40497725
X-RAY DIFFRACTIONf_chiral_restr0.0411814
X-RAY DIFFRACTIONf_plane_restr0.0019967
X-RAY DIFFRACTIONf_dihedral_angle_d11.62132157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.050.39391220.36562838X-RAY DIFFRACTION99.97
3.06-3.180.35351360.32882811X-RAY DIFFRACTION99.97
3.18-3.320.3331650.31832803X-RAY DIFFRACTION99.97
3.32-3.50.31271440.28072798X-RAY DIFFRACTION99.93
3.5-3.720.27261610.26572783X-RAY DIFFRACTION100
3.72-40.25381290.24172871X-RAY DIFFRACTION100
4-4.40.22761540.20422830X-RAY DIFFRACTION100
4.4-5.030.21091340.18522835X-RAY DIFFRACTION99.97
5.04-6.320.23231590.21582855X-RAY DIFFRACTION100
6.33-24.950.20251360.18982971X-RAY DIFFRACTION99.87

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