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

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Basic information

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


GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / diamine N-acetyltransferase / diamine 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
SPERMINE / Spermidine N1-acetyltransferase
Similarity search - Component
Biological speciesBacillus thuringiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsTsimbalyuk, S. / Shornikov, A. / Le, V.T.B. / Kuhn, M.L. / Forwood, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133506 United States
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
C: Spermidine N1-acetyltransferase
D: Spermidine N1-acetyltransferase
E: Spermidine N1-acetyltransferase
F: Spermidine N1-acetyltransferase
G: Spermidine N1-acetyltransferase
H: Spermidine N1-acetyltransferase
I: Spermidine N1-acetyltransferase
J: Spermidine N1-acetyltransferase
K: Spermidine N1-acetyltransferase
L: Spermidine N1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,84624
Polymers248,41812
Non-polymers2,42812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38930 Å2
ΔGint-41 kcal/mol
Surface area78480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.648, 125.595, 101.021
Angle α, β, γ (deg.)90.000, 106.500, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 and (name N or name...
21(chain B and (resid 4 through 5 or (resid 6...
31(chain C and ((resid 4 and (name N or name...
41(chain D and (resid 4 through 5 or (resid 6...
51(chain E and ((resid 4 and (name N or name...
61(chain F and (resid 4 through 5 or (resid 6...
71(chain G and (resid 4 through 5 or (resid 6...
81(chain H and ((resid 4 and (name N or name...
91(chain I and ((resid 4 and (name N or name...
101(chain J and ((resid 4 and (name N or name...
111(chain K and ((resid 4 and (name N or name...
121(chain L and (resid 4 through 5 or (resid 6...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLUGLU(chain A and ((resid 4 and (name N or name...AA44
12GLUGLUASNASN(chain A and ((resid 4 and (name N or name...AA4 - 1704 - 170
13GLUGLUASNASN(chain A and ((resid 4 and (name N or name...AA4 - 1704 - 170
14GLUGLUASNASN(chain A and ((resid 4 and (name N or name...AA4 - 1704 - 170
15GLUGLUASNASN(chain A and ((resid 4 and (name N or name...AA4 - 1704 - 170
21GLUGLULEULEU(chain B and (resid 4 through 5 or (resid 6...BB4 - 54 - 5
22LYSLYSLYSLYS(chain B and (resid 4 through 5 or (resid 6...BB66
23GLUGLUASNASN(chain B and (resid 4 through 5 or (resid 6...BB4 - 1704 - 170
24GLUGLUASNASN(chain B and (resid 4 through 5 or (resid 6...BB4 - 1704 - 170
25GLUGLUASNASN(chain B and (resid 4 through 5 or (resid 6...BB4 - 1704 - 170
26GLUGLUASNASN(chain B and (resid 4 through 5 or (resid 6...BB4 - 1704 - 170
31GLUGLUGLUGLU(chain C and ((resid 4 and (name N or name...CC44
32GLUGLUASNASN(chain C and ((resid 4 and (name N or name...CC4 - 1704 - 170
33GLUGLUASNASN(chain C and ((resid 4 and (name N or name...CC4 - 1704 - 170
34GLUGLUASNASN(chain C and ((resid 4 and (name N or name...CC4 - 1704 - 170
35GLUGLUASNASN(chain C and ((resid 4 and (name N or name...CC4 - 1704 - 170
41GLUGLULEULEU(chain D and (resid 4 through 5 or (resid 6...DD4 - 54 - 5
42LYSLYSLYSLYS(chain D and (resid 4 through 5 or (resid 6...DD66
43GLUGLUASNASN(chain D and (resid 4 through 5 or (resid 6...DD4 - 1704 - 170
51GLUGLUGLUGLU(chain E and ((resid 4 and (name N or name...EE44
52GLUGLUASNASN(chain E and ((resid 4 and (name N or name...EE4 - 1704 - 170
53GLUGLUASNASN(chain E and ((resid 4 and (name N or name...EE4 - 1704 - 170
54GLUGLUASNASN(chain E and ((resid 4 and (name N or name...EE4 - 1704 - 170
55GLUGLUASNASN(chain E and ((resid 4 and (name N or name...EE4 - 1704 - 170
61GLUGLULEULEU(chain F and (resid 4 through 5 or (resid 6...FF4 - 54 - 5
62LYSLYSLYSLYS(chain F and (resid 4 through 5 or (resid 6...FF66
63GLUGLUASNASN(chain F and (resid 4 through 5 or (resid 6...FF4 - 1704 - 170
64GLUGLUASNASN(chain F and (resid 4 through 5 or (resid 6...FF4 - 1704 - 170
65GLUGLUASNASN(chain F and (resid 4 through 5 or (resid 6...FF4 - 1704 - 170
66GLUGLUASNASN(chain F and (resid 4 through 5 or (resid 6...FF4 - 1704 - 170
71GLUGLULEULEU(chain G and (resid 4 through 5 or (resid 6...GG4 - 54 - 5
72LYSLYSLYSLYS(chain G and (resid 4 through 5 or (resid 6...GG66
73GLUGLUASNASN(chain G and (resid 4 through 5 or (resid 6...GG4 - 1704 - 170
81GLUGLUGLUGLU(chain H and ((resid 4 and (name N or name...HH44
82GLUGLUASNASN(chain H and ((resid 4 and (name N or name...HH4 - 1704 - 170
83GLUGLUASNASN(chain H and ((resid 4 and (name N or name...HH4 - 1704 - 170
84GLUGLUASNASN(chain H and ((resid 4 and (name N or name...HH4 - 1704 - 170
85GLUGLUASNASN(chain H and ((resid 4 and (name N or name...HH4 - 1704 - 170
91GLUGLUGLUGLU(chain I and ((resid 4 and (name N or name...II44
92GLUGLUASNASN(chain I and ((resid 4 and (name N or name...II4 - 1704 - 170
93GLUGLUASNASN(chain I and ((resid 4 and (name N or name...II4 - 1704 - 170
94GLUGLUASNASN(chain I and ((resid 4 and (name N or name...II4 - 1704 - 170
95GLUGLUASNASN(chain I and ((resid 4 and (name N or name...II4 - 1704 - 170
101GLUGLUGLUGLU(chain J and ((resid 4 and (name N or name...JJ44
102GLUGLUASNASN(chain J and ((resid 4 and (name N or name...JJ4 - 1704 - 170
103GLUGLUASNASN(chain J and ((resid 4 and (name N or name...JJ4 - 1704 - 170
104GLUGLUASNASN(chain J and ((resid 4 and (name N or name...JJ4 - 1704 - 170
105GLUGLUASNASN(chain J and ((resid 4 and (name N or name...JJ4 - 1704 - 170
111GLUGLUGLUGLU(chain K and ((resid 4 and (name N or name...KK44
112GLUGLUASNASN(chain K and ((resid 4 and (name N or name...KK4 - 1704 - 170
113GLUGLUASNASN(chain K and ((resid 4 and (name N or name...KK4 - 1704 - 170
114GLUGLUASNASN(chain K and ((resid 4 and (name N or name...KK4 - 1704 - 170
115GLUGLUASNASN(chain K and ((resid 4 and (name N or name...KK4 - 1704 - 170
121GLUGLULEULEU(chain L and (resid 4 through 5 or (resid 6...LL4 - 54 - 5
122LYSLYSLYSLYS(chain L and (resid 4 through 5 or (resid 6...LL66
123GLUGLUASNASN(chain L and (resid 4 through 5 or (resid 6...LL4 - 1704 - 170
124GLUGLUASNASN(chain L and (resid 4 through 5 or (resid 6...LL4 - 1704 - 170
125GLUGLUASNASN(chain L and (resid 4 through 5 or (resid 6...LL4 - 1704 - 170
126GLUGLUASNASN(chain L and (resid 4 through 5 or (resid 6...LL4 - 1704 - 170

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Components

#1: Protein
Spermidine N1-acetyltransferase / Spermidine acetyltransferase


Mass: 20701.477 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis (bacteria)
Gene: speG, BJG91_21635, BK774_28255, BK775_18720, C5676_03263, CBR59_17915, D7J84_13550
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0G3E2X5, diamine N-acetyltransferase, GMP synthase (glutamine-hydrolysing)
#2: Chemical
ChemComp-SPM / SPERMINE


Mass: 202.340 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H26N4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 30% ethanol

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→29.87 Å / Num. obs: 83267 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.056 / Rrim(I) all: 0.138 / Net I/σ(I): 10.4 / Num. measured all: 488797 / Scaling rejects: 110
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
2.5-2.5560.9952719645680.6620.4461.0921.9100
12.99-29.876.10.04935355820.9960.0220.05429.892.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.87 Å
Translation2.5 Å29.87 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIXrefinement version: 1.13_2998refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WR7

3wr7


Resolution: 2.5→29.869 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.76
RfactorNum. reflection% reflection
Rfree0.2522 4214 5.06 %
Rwork0.2259 --
obs0.2272 83235 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.8 Å2 / Biso mean: 42.9283 Å2 / Biso min: 18.29 Å2
Refinement stepCycle: final / Resolution: 2.5→29.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16767 0 168 0 16935
Biso mean--37.39 --
Num. residues----2004
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A9658X-RAY DIFFRACTION9.605TORSIONAL
12B9658X-RAY DIFFRACTION9.605TORSIONAL
13C9658X-RAY DIFFRACTION9.605TORSIONAL
14D9658X-RAY DIFFRACTION9.605TORSIONAL
15E9658X-RAY DIFFRACTION9.605TORSIONAL
16F9658X-RAY DIFFRACTION9.605TORSIONAL
17G9658X-RAY DIFFRACTION9.605TORSIONAL
18H9658X-RAY DIFFRACTION9.605TORSIONAL
19I9658X-RAY DIFFRACTION9.605TORSIONAL
110J9658X-RAY DIFFRACTION9.605TORSIONAL
111K9658X-RAY DIFFRACTION9.605TORSIONAL
112L9658X-RAY DIFFRACTION9.605TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5-2.52840.32561330.29412660
2.5284-2.55810.33011180.30532640
2.5581-2.58930.35821190.30282629
2.5893-2.62210.34841250.3072625
2.6221-2.65660.35421290.31142644
2.6566-2.69290.35841430.29832611
2.6929-2.73140.35811450.29462673
2.7314-2.77210.35431300.28572568
2.7721-2.81540.34511590.28872625
2.8154-2.86150.30091410.26892629
2.8615-2.91080.29231750.27892568
2.9108-2.96370.34921400.28152663
2.9637-3.02070.33091250.28822607
3.0207-3.08220.32561590.29322609
3.0822-3.14920.34031470.28432634
3.1492-3.22240.33611310.27582645
3.2224-3.30290.26911300.2612635
3.3029-3.3920.29611470.25382605
3.392-3.49170.24561370.23452655
3.4917-3.60420.27931570.23482616
3.6042-3.73280.23861630.22352617
3.7328-3.8820.23341550.21552616
3.882-4.05820.22761470.19542629
4.0582-4.27160.19071570.18052606
4.2716-4.53840.16631120.16272664
4.5384-4.88740.17771070.16482692
4.8874-5.37670.17381660.17592619
5.3767-6.14880.24951300.21122655
6.1488-7.72460.22111400.20362681
7.7246-29.8690.16521470.15962701

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