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- PDB-6vfm: Crystal structure of SpeG allosteric polyamine acetyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 6vfm
TitleCrystal structure of SpeG allosteric polyamine acetyltransferase from Bacillus thuringiensis
ComponentsSpermidine N1-acetyltransferase
KeywordsTRANSFERASE / SpeG / Allosteric enzyme / GNAT
Function / homology
Function and homology information


diamine N-acetyltransferase activity / N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GNAT family N-acetyltransferase / Spermidine N1-acetyltransferase
Similarity search - Component
Biological speciesBacillus thuringiensis subsp. finitimus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.67 Å
AuthorsTsimbalyuk, S. / Shornikov, A. / Le, V.T.B. / Kuhn, M.L. / Forwood, J.K.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: SpeG polyamine acetyltransferase enzyme from Bacillus thuringiensis forms a dodecameric structure and exhibits high catalytic efficiency.
Authors: Tsimbalyuk, S. / Shornikov, A. / Thi Bich Le, V. / Kuhn, M.L. / Forwood, J.K.
History
DepositionJan 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)41,2932
Polymers41,2932
Non-polymers00
Water00
1
A: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
x 6


Theoretical massNumber of molelcules
Total (without water)247,75712
Polymers247,75712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area32120 Å2
ΔGint-132 kcal/mol
Surface area84930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.374, 159.374, 106.205
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 7 - 173 / Label seq-ID: 4 - 170

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Spermidine N1-acetyltransferase


Mass: 20646.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis subsp. finitimus (strain YBT-020) (bacteria)
Strain: YBT-020 / Gene: YBT020_25265 / Production host: Escherichia coli (E. coli) / References: UniProt: F0PQY5, UniProt: A0A437SL45*PLUS

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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: 4.75 Å3/Da / Density % sol: 74.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: TRIS pH7.5, PEG4000, and 0.2 M Lithium sulfate

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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 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.67→63.74 Å / Num. obs: 23127 / % possible obs: 100 % / Redundancy: 25.5 % / Biso Wilson estimate: 42.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.318 / Rpim(I) all: 0.065 / Rrim(I) all: 0.325 / Net I/σ(I): 8.1 / Num. measured all: 589520 / Scaling rejects: 51
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.67-2.827.11.4998125930010.7340.2971.5293.2100
8.86-63.7422.10.077162977380.9990.0170.07915.999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.99 Å53.1 Å

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WR7

3wr7


Resolution: 2.67→63.74 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2931 1169 5.08 %
Rwork0.2744 21861 -
obs0.2753 23030 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.56 Å2 / Biso mean: 45.32 Å2 / Biso min: 10.1 Å2
Refinement stepCycle: final / Resolution: 2.67→63.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 0 0 2842
Num. residues----334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032912
X-RAY DIFFRACTIONf_angle_d0.6433926
X-RAY DIFFRACTIONf_chiral_restr0.046402
X-RAY DIFFRACTIONf_plane_restr0.004514
X-RAY DIFFRACTIONf_dihedral_angle_d4.5281728
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1656X-RAY DIFFRACTION8.925TORSIONAL
12B1656X-RAY DIFFRACTION8.925TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6701-2.79160.42221370.40012674100
2.7916-2.93880.39851470.37222682100
2.9388-3.12290.39591250.33432715100
3.1229-3.3640.32351640.28992683100
3.364-3.70250.2951420.27332699100
3.7025-4.23810.24621530.23312730100
4.2381-5.33920.22911380.2162788100
5.3392-63.740.26151630.2569289099

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