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- PDB-4jjx: Dodecameric structure of spermidine N-acetyltransferase SpeG from... -

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Basic information

Entry
Database: PDB / ID: 4jjx
TitleDodecameric structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae O1 biovar eltor
ComponentsSpermidine n1-acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
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) domain / Acetyltransferase (GNAT) family / 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
Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Kuhn, M.L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Mol.Biol. / Year: 2015
Title: A Novel Polyamine Allosteric Site of SpeG from Vibrio cholerae Is Revealed by Its Dodecameric Structure.
Authors: Filippova, E.V. / Kuhn, M.L. / Osipiuk, J. / Kiryukhina, O. / Joachimiak, A. / Ballicora, M.A. / Anderson, W.F.
History
DepositionMar 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)62,9273
Polymers62,9273
Non-polymers00
Water46826
1
A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)251,70812
Polymers251,70812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area31500 Å2
ΔGint-80 kcal/mol
Surface area84300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.524, 131.524, 72.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Spermidine n1-acetyltransferase


Mass: 20975.646 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q9KL03
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 45% Ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2012 / Details: Beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.82→30 Å / Num. all: 15565 / Num. obs: 15565 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 68.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.4
Reflection shellResolution: 2.82→2.87 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2 / Num. unique all: 1469 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EG7

3eg7
PDB Unreleased entry


Resolution: 2.83→29.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 36.217 / SU ML: 0.321 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26479 774 5 %RANDOM
Rwork0.19372 ---
obs0.19729 14686 98.21 %-
all-14686 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.29 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å2-0 Å2
2---1.64 Å20 Å2
3---3.29 Å2
Refinement stepCycle: LAST / Resolution: 2.83→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 0 26 4314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194398
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9345938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98923.977264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.32315771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9361535
X-RAY DIFFRACTIONr_chiral_restr0.0960.2626
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023439
LS refinement shellResolution: 2.83→2.903 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 54 -
Rwork0.303 1048 -
obs--96.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5466-0.14332.205210.04882.06633.78140.02670.3549-0.292-0.1404-0.1540.6296-0.206-0.1370.12730.1233-0.0050.05670.1494-0.10280.2623-17.0793-21.617313.1656
23.75791.68821.168911.9817-2.52074.74940.5883-0.46040.81780.9233-0.38911.1032-0.9697-0.0043-0.19920.4165-0.05550.22420.1987-0.14230.2942-17.5816-12.761224.6033
31.77381.2322-2.81834.945-3.227510.62180.26860.10250.2088-0.0884-0.30980.0647-0.46830.31640.04120.07070.03360.0140.1165-0.06440.2831-18.3107-28.096518.9647
42.5584-2.0672-2.14852.32040.74453.41950.1310.2335-0.3361-0.2064-0.25120.4281-0.0298-0.01490.12010.1193-0.057-0.08890.1137-0.03560.2116-26.9803-32.860727.2077
55.706-0.07491.65753.0302-0.53793.54030.07080.14650.08280.035-0.02490.390.4162-0.3889-0.04590.143-0.0834-0.01750.07860.01240.06925.4406-22.592221.2337
64.7317-0.31482.96462.6896-2.638212.6526-0.06880.3108-0.3309-0.4689-0.0607-0.1211-0.2307-0.29910.12950.1350.03220.0270.069-0.0530.063613.8261-29.147319.885
74.81049.54520.309521.3558-8.409433.7762-0.5849-0.0860.2436-1.3638-0.42320.2190.74270.76191.00810.42260.25350.06710.3926-0.13060.233614.6595-38.956810.0602
83.52212.1725-0.59222.8904-0.2712.92880.06730.4485-0.4419-0.14160.0017-0.34960.17530.3546-0.0690.04670.074-0.01890.1783-0.06110.088814.1374-40.193326.7441
98.84788.73373.41149.20496.283515.8949-0.3260.3161-1.3257-0.17610.76-1.3140.96932.0496-0.4340.38890.23390.17220.9249-0.11350.664931.0654-38.51824.2964
104.39721.96490.743116.58252.48390.72620.7458-1.22110.16550.6008-0.90150.07890.0554-0.1230.15570.2939-0.17040.01350.5190.00460.10363.9308-26.406259.8358
118.06654.36211.02634.3142.8638.94070.6204-0.170.64840.0105-0.2913-0.33370.4854-0.007-0.32910.32630.01940.18640.20830.06980.339811.2084-20.806349.4374
120.5714-0.2485-2.2526.2349-4.390126.81060.0916-0.2042-0.0654-0.00330.15540.72080.6224-0.3822-0.2470.0972-0.14290.03680.2692-0.10550.2553-0.5603-26.876954.805
132.2871.97382.75333.00771.267512.60710.0613-0.45860.12870.5666-0.40240.17720.1089-0.37760.34110.2374-0.02830.04340.1641-0.02170.01773.1697-36.272652.865
145.8725-0.30231.04540.98550.00283.39970.4331-0.4276-0.47770.3781-0.2753-0.14060.5808-0.4045-0.15780.2837-0.1932-0.10820.16030.07990.10928.3161-42.770945.6432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 25
2X-RAY DIFFRACTION2A26 - 53
3X-RAY DIFFRACTION3A54 - 104
4X-RAY DIFFRACTION4A105 - 170
5X-RAY DIFFRACTION5B4 - 57
6X-RAY DIFFRACTION6B58 - 93
7X-RAY DIFFRACTION7B94 - 100
8X-RAY DIFFRACTION8B101 - 167
9X-RAY DIFFRACTION9B168 - 171
10X-RAY DIFFRACTION10C2 - 23
11X-RAY DIFFRACTION11C24 - 48
12X-RAY DIFFRACTION12C49 - 66
13X-RAY DIFFRACTION13C67 - 108
14X-RAY DIFFRACTION14C109 - 170

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