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- PDB-8fv0: SpeG spermidine N-acetyltransferase from Staphylococcus aureus in... -

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Basic information

Entry
Database: PDB / ID: 8fv0
TitleSpeG spermidine N-acetyltransferase from Staphylococcus aureus in complex with spermine
ComponentsDiamine N-acetyltransferase
KeywordsTRANSFERASE
Function / homologyAcetyltransferase (GNAT) domain / 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: 2.65 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
Authors: Tsimbalyuk, S. / Forwood, J.K.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
SupersessionApr 26, 2023ID: 7KY3
Revision 1.0Apr 26, 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
B: Diamine N-acetyltransferase
A: Diamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8416
Polymers60,2343
Non-polymers6073
Water00
1
C: Diamine N-acetyltransferase
B: Diamine N-acetyltransferase
A: Diamine N-acetyltransferase
hetero molecules

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

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

C: Diamine N-acetyltransferase
B: Diamine N-acetyltransferase
A: 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 operation2_555-x,-y,z1
crystal symmetry operation3_554-x,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Unit cell
Length a, b, c (Å)68.098, 119.951, 145.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Diamine N-acetyltransferase


Mass: 20077.939 Da / Num. of mol.: 3
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.: 3 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NaCl, 0.1 M HEPES pH 8.0, and 1.6 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.65→24.86 Å / Num. obs: 17700 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 41.04 Å2 / CC1/2: 0.775 / Rmerge(I) obs: 0.14 / Net I/σ(I): 2.4
Reflection shellResolution: 2.64→2.65 Å / Num. unique obs: 871 / CC1/2: 0.775

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→24.86 Å / SU ML: 0.2748 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2677 871 4.92 %
Rwork0.2205 16819 -
obs0.2226 17690 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.64 Å2
Refinement stepCycle: LAST / Resolution: 2.65→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 42 0 4214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024313
X-RAY DIFFRACTIONf_angle_d0.43495792
X-RAY DIFFRACTIONf_chiral_restr0.0409608
X-RAY DIFFRACTIONf_plane_restr0.002724
X-RAY DIFFRACTIONf_dihedral_angle_d11.57911608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.820.28921710.26552716X-RAY DIFFRACTION99.93
2.82-3.030.33791320.27792796X-RAY DIFFRACTION99.97
3.03-3.340.30971540.25462750X-RAY DIFFRACTION99.9
3.34-3.820.28671440.22872788X-RAY DIFFRACTION99.97
3.82-4.810.22241360.17972831X-RAY DIFFRACTION100
4.81-24.860.23311340.20512938X-RAY DIFFRACTION99.84

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