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- PDB-7kwh: Spermidine N-acetyltransferase SpeG K23-Y30 chimera from Vibrio c... -

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Basic information

Entry
Database: PDB / ID: 7kwh
TitleSpermidine N-acetyltransferase SpeG K23-Y30 chimera from Vibrio cholerae and hSSAT
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
PHOSPHATE ION / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLe, V.T.B. / Tsimbalyuk, S. / Lim, E.Q. / Solis, A. / Gawat, D. / Boeck, P. / Renolo, R. / Forwood, J.K.
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 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 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 1.3Oct 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
D: Spermidine N(1)-acetyltransferase
E: Spermidine N(1)-acetyltransferase
F: Spermidine N(1)-acetyltransferase
J: Spermidine N(1)-acetyltransferase
L: Spermidine N(1)-acetyltransferase
K: Spermidine N(1)-acetyltransferase
G: Spermidine N(1)-acetyltransferase
H: Spermidine N(1)-acetyltransferase
I: Spermidine N(1)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,93320
Polymers249,17412
Non-polymers7608
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32730 Å2
ΔGint-117 kcal/mol
Surface area84250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.450, 156.530, 188.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Spermidine N(1)-acetyltransferase / SAT / Spermidine/spermine N(1)-acetyltransferase / SSAT


Mass: 20764.463 Da / Num. of mol.: 12 / Mutation: N23K, N24E, R25L, N26A, I27R, M28Y, S29E
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
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
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: 3.13 Å3/Da / Density % sol: 60.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES pH6.5, 10% PEG5000 MME, and 12% propanol

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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: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.9→39.68 Å / Num. obs: 69880 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 66.24 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.9
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.621 / Mean I/σ(I) obs: 2 / Num. unique obs: 4434 / CC1/2: 0.509 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASER1.18.2_3874phasing
PHENIX1.18.2_3874refinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJX

4jjx


Resolution: 2.9→39.68 Å / SU ML: 0.4392 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.12
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2546 3565 5.11 %
Rwork0.2179 66225 -
obs0.2198 69790 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.25 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16922 0 40 0 16962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001417349
X-RAY DIFFRACTIONf_angle_d0.364623426
X-RAY DIFFRACTIONf_chiral_restr0.04142466
X-RAY DIFFRACTIONf_plane_restr0.00133056
X-RAY DIFFRACTIONf_dihedral_angle_d18.01086416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.34351500.31072592X-RAY DIFFRACTION99.82
2.94-2.980.38541390.31432597X-RAY DIFFRACTION99.96
2.98-3.030.36331320.30932669X-RAY DIFFRACTION99.93
3.03-3.070.34321320.29622597X-RAY DIFFRACTION99.96
3.07-3.120.35461510.27232628X-RAY DIFFRACTION99.82
3.12-3.180.30381480.26362619X-RAY DIFFRACTION99.86
3.18-3.240.34631240.27372590X-RAY DIFFRACTION99.71
3.24-3.30.30621380.26962652X-RAY DIFFRACTION99.71
3.3-3.360.35241250.27112634X-RAY DIFFRACTION100
3.36-3.440.33811560.27972600X-RAY DIFFRACTION99.93
3.44-3.520.3141450.25512635X-RAY DIFFRACTION99.96
3.52-3.610.29711670.2372627X-RAY DIFFRACTION100
3.61-3.70.25791380.2222615X-RAY DIFFRACTION99.82
3.7-3.810.26751400.20322641X-RAY DIFFRACTION99.82
3.81-3.940.25611480.20732629X-RAY DIFFRACTION99.89
3.94-4.080.24581380.19352631X-RAY DIFFRACTION99.86
4.08-4.240.19981340.1762666X-RAY DIFFRACTION99.72
4.24-4.430.18781270.17342648X-RAY DIFFRACTION99.93
4.43-4.660.20191420.16612650X-RAY DIFFRACTION99.96
4.66-4.960.19351430.16872680X-RAY DIFFRACTION99.96
4.96-5.340.18621470.16722681X-RAY DIFFRACTION99.93
5.34-5.870.22341560.20292676X-RAY DIFFRACTION100
5.87-6.720.29471690.24392665X-RAY DIFFRACTION99.93
6.72-8.450.2541400.23792738X-RAY DIFFRACTION100
8.45-39.680.2221360.21252865X-RAY DIFFRACTION99.54

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