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- PDB-7kwx: Spermidine N-acetyltransferase SpeG N152L mutant from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 7kwx
TitleSpermidine N-acetyltransferase SpeG N152L 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: 2.42 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 2, 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)62,1073
Polymers62,1073
Non-polymers00
Water00
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)248,42912
Polymers248,42912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_454-x-1,y,-z-11
crystal symmetry operation4_554x,-y,-z-11
Buried area32280 Å2
ΔGint-92 kcal/mol
Surface area82550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.020, 135.940, 139.400
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: 20702.441 Da / Num. of mol.: 3 / Mutation: N152L
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 (E. coli) / References: UniProt: Q9KL03, diamine N-acetyltransferase

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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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 10% ethanol

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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: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.42→48.66 Å / Num. obs: 26869 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 46.32 Å2 / CC1/2: 0.998 / Net I/σ(I): 16.1
Reflection shellResolution: 2.42→2.507 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2762 / CC1/2: 0.778

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Processing

Software
NameVersionClassification
Coot1.18.2_3874model building
PHENIX1.18.2_3874refinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJX

4jjx


Resolution: 2.42→47.27 Å / SU ML: 0.3573 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.7465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2727 1374 5.12 %
Rwork0.2241 25485 -
obs0.2265 26859 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.16 Å2
Refinement stepCycle: LAST / Resolution: 2.42→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 0 0 4307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164406
X-RAY DIFFRACTIONf_angle_d0.40185949
X-RAY DIFFRACTIONf_chiral_restr0.0427630
X-RAY DIFFRACTIONf_plane_restr0.0012778
X-RAY DIFFRACTIONf_dihedral_angle_d24.06391639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.510.38111320.31512495X-RAY DIFFRACTION99.7
2.51-2.610.33431370.28542515X-RAY DIFFRACTION100
2.61-2.730.34691470.28052516X-RAY DIFFRACTION99.89
2.73-2.870.33351310.2792514X-RAY DIFFRACTION100
2.87-3.050.40451270.29362546X-RAY DIFFRACTION99.96
3.05-3.280.29411220.26692532X-RAY DIFFRACTION100
3.28-3.610.27761200.2452564X-RAY DIFFRACTION100
3.61-4.140.23351770.20132532X-RAY DIFFRACTION99.93
4.14-5.210.23961200.16442603X-RAY DIFFRACTION100
5.21-47.270.2271610.19652668X-RAY DIFFRACTION99.86

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