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- PDB-7kx2: Spermidine N-acetyltransferase SpeG F149A mutant from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 7kx2
TitleSpermidine N-acetyltransferase SpeG F149A mutant from Vibrio cholerae
ComponentsSpermidine N(1)-acetyltransferase
KeywordsTRANSFERASE / SpeG Enzyme Allosteric
Function / homology
Function and homology information


polyamine catabolic process / spermine catabolic process / spermidine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLe, V.T.B. / Tsimbalyuk, S. / Lim, E.Q. / Solis, A. / Gawat, D. / Boeck, P. / Renolo, R. / Forwood, J.K. / Kuhn, M.L.
CitationJournal: Front Mol Biosci / Year: 2021
Title: The Vibrio cholerae SpeG Spermidine/Spermine N -Acetyltransferase Allosteric Loop and beta 6-beta 7 Structural Elements Are Critical for Kinetic Activity.
Authors: Le, V.T.B. / Tsimbalyuk, S. / Lim, E.Q. / Solis, A. / Gawat, D. / Boeck, P. / Lim, E.Q. / Renolo, R. / Forwood, J.K. / Kuhn, M.L.
History
DepositionDec 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)61,8823
Polymers61,8823
Non-polymers00
Water905
1
A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase

A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase

A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase

A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)247,52712
Polymers247,52712
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)73.435, 135.942, 139.519
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 Spermidine N(1)-acetyltransferase / SAT / Spermidine/spermine N(1)-acetyltransferase / SSAT


Mass: 20627.289 Da / Num. of mol.: 3 / Mutation: F149A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: speG, VC_A0947 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KL03, diamine N-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium chloride pH 7.0, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→48.68 Å / Num. obs: 21877 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 77.49 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.7
Reflection shellResolution: 2.6→2.693 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2623 / CC1/2: 0.484

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Processing

Software
NameVersionClassification
PDB_EXTRACT1.18.2_3874data extraction
PHENIX1.18.2_3874refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJX

4jjx


Resolution: 2.6→47.4 Å / SU ML: 0.5326 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.8843
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3079 1165 5.33 %
Rwork0.25 20709 -
obs0.253 21874 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.9 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4238 0 0 5 4243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00134334
X-RAY DIFFRACTIONf_angle_d0.35785855
X-RAY DIFFRACTIONf_chiral_restr0.0417621
X-RAY DIFFRACTIONf_plane_restr0.001768
X-RAY DIFFRACTIONf_dihedral_angle_d20.61281610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.4161580.36852522X-RAY DIFFRACTION99.96
2.72-2.860.44171320.34582558X-RAY DIFFRACTION100
2.86-3.040.42911540.33592548X-RAY DIFFRACTION99.96
3.04-3.280.33591380.29672570X-RAY DIFFRACTION100
3.28-3.610.35651220.2832598X-RAY DIFFRACTION99.96
3.61-4.130.31881420.24842590X-RAY DIFFRACTION100
4.13-5.20.26821770.21212594X-RAY DIFFRACTION100
5.2-47.40.27271420.22612729X-RAY DIFFRACTION99.9

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