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- PDB-4ygo: Dodecameric structure of spermidine N-acetyltransferase from Vibr... -

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Basic information

Entry
Database: PDB / ID: 4ygo
TitleDodecameric structure of spermidine N-acetyltransferase from Vibrio cholerae in intermediate state
ComponentsSpermidine n1-acetyltransferase
KeywordsTRANSFERASE / SpeG / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


spermidine catabolic process / polyamine catabolic process / spermine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / magnesium ion binding / cytoplasm
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
METHANOL / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFilippova, E.V. / Minasov, G. / Kiryukhina, O. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Substrate-Induced Allosteric Change in the Quaternary Structure of the Spermidine N-Acetyltransferase SpeG.
Authors: Filippova, E.V. / Weigand, S. / Osipiuk, J. / Kiryukhina, O. / Joachimiak, A. / Anderson, W.F.
History
DepositionFeb 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.5Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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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
D: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
E: Spermidine n1-acetyltransferase
F: Spermidine n1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,49313
Polymers124,2206
Non-polymers2737
Water2,594144
1
A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
D: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
E: Spermidine n1-acetyltransferase
F: Spermidine n1-acetyltransferase
hetero molecules

A: Spermidine n1-acetyltransferase
B: Spermidine n1-acetyltransferase
D: Spermidine n1-acetyltransferase
C: Spermidine n1-acetyltransferase
E: Spermidine n1-acetyltransferase
F: Spermidine n1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,98626
Polymers248,44112
Non-polymers54514
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area32660 Å2
ΔGint-202.7 kcal/mol
Surface area84450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.118, 135.793, 72.848
Angle α, β, γ (deg.)90.00, 117.13, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.572187, -0.040617, -0.819116), (0.048787, -0.99869, 0.015441), (-0.81867, -0.031127, 0.573419)4.72499, 178.90036, 2.0502
3given(-0.158355, -0.781637, -0.603298), (0.77485, -0.477083, 0.414727), (-0.611989, -0.401791, 0.6812)70.63577, 131.01723, 35.26604
4given(0.62751, -0.758127, -0.177412), (0.747195, 0.522282, 0.411001), (-0.218931, -0.390469, 0.894205)67.11399, 40.35147, 33.76793
5given(0.63343, 0.743532, -0.214305), (-0.759131, 0.543445, -0.358311), (-0.149952, 0.389651, 0.908673)-64.79691, 39.72213, -32.54556
6given(-0.234689, 0.709998, -0.663946), (-0.707463, -0.593172, -0.384244), (-0.666646, 0.379539, 0.641508)-60.5214, 141.73587, -32.84689

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Components

#1: Protein
Spermidine n1-acetyltransferase


Mass: 20703.385 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_A0947 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q9KL03
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: CH4O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.01 M CaCl2, 0.1 M Tris HCl, 20% Methanol, 25 % MPD

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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: Dec 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 46610 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 54.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
BLU-MAXdata collection
HKL-3000data scaling
PHASERphasing
Cootmodel building
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EG7

3eg7
PDB Unreleased entry


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 20.949 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.448 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25274 2408 5.2 %RANDOM
Rwork0.18011 ---
obs0.18368 44197 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.62 Å2
Baniso -1Baniso -2Baniso -3
1--3.99 Å2-0 Å2-1.54 Å2
2--0.6 Å2-0 Å2
3---3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8611 0 8 144 8763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0198821
X-RAY DIFFRACTIONr_bond_other_d0.0020.028303
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.93511891
X-RAY DIFFRACTIONr_angle_other_deg1.052318956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.20251011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80524.011531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.511151554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1581569
X-RAY DIFFRACTIONr_chiral_restr0.1040.21252
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210108
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022309
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9793.9344069
X-RAY DIFFRACTIONr_mcbond_other1.9783.9344067
X-RAY DIFFRACTIONr_mcangle_it3.0695.8895069
X-RAY DIFFRACTIONr_mcangle_other3.0695.8895070
X-RAY DIFFRACTIONr_scbond_it2.5324.2034752
X-RAY DIFFRACTIONr_scbond_other2.5324.2044753
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8466.2116823
X-RAY DIFFRACTIONr_long_range_B_refined5.58730.9969704
X-RAY DIFFRACTIONr_long_range_B_other5.5830.9619691
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.556 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 183 -
Rwork0.279 3013 -
obs--92.72 %
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)
14.6781-1.72281.50145.84171.84885.80730.23970.4346-0.1009-0.5687-0.12-0.20760.0478-0.5253-0.11960.2143-0.04820.08330.1998-0.01430.0488-29.276-21.93570.3547
24.64870.52440.42134.58680.34160.4713-0.3906-0.32270.2960.19210.1999-0.0602-0.1078-0.11340.19070.2134-0.00180.01790.1031-0.07510.1721-30.8919-13.660311.396
34.6208-0.0537-0.98482.4528-1.87837.630.03850.3263-0.4523-0.36480.00240.06510.5751-0.0293-0.04090.1455-0.02350.03150.0739-0.01880.1031-32.0261-25.67133.9822
47.81111.9539-2.71025.0099-1.78934.49430.16170.0295-0.07680.1582-0.52210.05110.20480.16050.36030.0807-0.05630.00310.1421-0.01890.1053-44.5451-27.981514.556
55.22073.22160.24265.299-1.69464.8893-0.24090.82180.0255-0.75260.29090.35890.2746-0.065-0.05010.2932-0.00640.0260.3143-0.01430.0918-40.2016-25.0044-4.0128
61.3326-0.2007-0.04723.7303-0.26632.55710.01180.3069-0.0118-0.555-0.10750.40710.1108-0.32670.09570.1108-0.0599-0.05370.2639-0.03390.0512-51.121-21.08194.043
73.15070.43331.77797.4468-1.63882.4170.0436-0.1088-0.3544-0.7465-0.0208-0.38280.13110.543-0.02280.2488-0.01330.1210.42170.06840.162916.1105-15.929224.8781
82.0143-1.79312.7725.5911-0.43524.86520.2223-0.0106-0.1761-0.2418-0.13280.35970.2953-0.0441-0.08960.15190.03060.08730.15080.09310.1657.9567-23.287732.8345
90.59420.7998-0.15392.22321.4946.26840.02580.11570.0922-0.1244-0.0345-0.175-0.27160.45930.00880.08470.03570.03260.31180.09380.208615.9087-11.379634.5745
106.27470.0391-2.56558.41875.16127.0394-0.17210.1636-0.2125-0.13270.1852-0.6183-0.26880.6531-0.01310.08190.02740.04160.37390.09260.154127.0873-13.717330.3925
111.133-0.624-0.05623.5553-0.37871.5596-0.14080.02690.0647-0.03020.0637-0.5745-0.01210.46660.07710.03030.00520.03520.29650.02870.17925.6544-15.443844.7311
126.73672.67670.73792.7749-0.40171.99040.05240.5002-0.0098-0.1452-0.108-0.1794-0.00790.31370.05560.1542-0.0470.04550.14480.02420.172.73624.595417.5654
136.4756-0.44560.69121.24791.123.19290.1004-0.0665-0.16970.2864-0.07060.1160.24830.228-0.02980.1663-0.0249-0.03090.0567-0.00220.14980.8716-1.8629.2734
143.8166-1.67-3.60162.07482.07526.9754-0.00070.18170.257-0.09840.202-0.0403-0.44530.1746-0.20130.1352-0.0969-0.02410.11590.01890.1535-2.014610.877424.3561
151.16091.3571-0.47044.084-4.52388.785-0.02040.0840.0815-0.5387-0.1814-0.21070.03750.30910.20180.4821-0.06420.10860.30330.03320.34319.860715.852517.752
166.2601-0.43441.43530.5806-0.98412.8762-0.09680.25190.3929-0.0462-0.0834-0.0605-0.42010.21040.18020.287-0.0809-0.01310.07360.0240.21531.749820.631928.4894
172.1561-2.65671.94383.855-2.20982.602-0.14490.11820.4161-0.007-0.1627-0.2659-0.4060.34080.30760.2938-0.1097-0.04250.11010.00460.27265.092819.411636.1475
182.31111.2069-0.26841.23510.94235.7719-0.25440.4773-0.1339-0.36540.2059-0.2927-0.3227-0.24580.04850.2926-0.0260.07080.17980.04520.2344-20.06171.1295.11
192.8368-0.23780.37935.31954.63044.16030.08750.25240.3768-0.12070.146-0.3818-0.13390.1567-0.23360.25830.0837-0.05160.1022-0.02020.2427-17.98888.52817.5675
208.03393.2213-1.04273.14650.93831.2154-0.1772-0.1764-0.37580.10210.1626-0.34230.06710.17370.01460.18340.0099-0.05770.0888-0.0240.2073-17.1853-2.382619.2423
213.9895-2.2079-0.55792.78141.75911.42990.26260.27640.1645-0.5738-0.154-0.1668-0.4376-0.0504-0.10860.27830.02310.02820.06950.0670.0825-28.85543.286110.3254
222.30370.57840.41420.9585-0.56181.411-0.1340.17920.1063-0.3184-0.07240.0176-0.2080.13750.20640.36940.0493-0.01940.11790.07160.19-30.829110.84976.6021
233.01961.0462.97110.78091.43534.5252-0.29570.34270.2424-0.20510.0561-0.0137-0.4330.15760.23960.3010.0573-0.05610.09980.06580.1838-33.872418.767712.8965
244.59371.4913-0.40886.92860.87592.00450.08680.4689-0.05350.0577-0.3744-0.70440.12030.170.28760.1501-0.03660.05960.18410.08340.1793-15.5718-43.04948.3224
254.79190.68522.05085.8298-1.0231.5301-0.0688-0.17980.05740.2011-0.08480.11270.1344-0.18340.15370.156-0.09540.06840.10550.00210.1286-24.6318-37.116314.9753
262.64441.1828-3.70263.7792-2.15216.9256-0.1479-0.0304-0.21740.1302-0.0155-0.51810.35710.12340.16340.0856-0.0427-0.02630.10020.01470.1293-19.0894-50.490914.9495
272.6992-0.6425-0.20572.5464-0.11134.15480.23680.1192-0.31940.0695-0.2697-0.27260.35030.36780.03290.2409-0.0166-0.00020.07360.00720.1012-23.0353-56.903910.0333
284.3318-1.3127-0.010.43520.50368.8805-0.17640.33350.01550.1019-0.08990.00110.2655-0.24260.26630.19750.0034-0.00320.1587-0.02810.1765-30.0018-63.14626.8979
296.0921-2.57331.19523.60410.1441.60050.4093-0.2175-0.7469-0.1583-0.10580.45020.3513-0.0452-0.30350.3645-0.11430.02870.068-0.0390.1815-34.4258-57.605514.7736
305.85140.53421.48914.8811-1.11524.75590.02030.7036-0.7427-0.37850.20160.23460.6067-0.0937-0.22190.2130.05190.0350.1691-0.04190.13951.4047-42.271422.9531
313.7303-1.4268-3.1172.528-0.38476.2309-0.13110.5167-0.1362-0.15860.00030.16060.27010.09740.13090.2290.02930.05470.32250.01610.1184.9667-37.696325.5576
322.59441.28411.13410.95471.71368.40970.0674-0.0169-0.0368-0.1835-0.0916-0.1633-0.1068-0.30410.02420.32840.12630.13440.117-0.00040.20126.7772-42.66440.8044
331.99770.11281.04251.9145-0.05312.6311-0.01070.4382-0.2574-0.2577-0.1797-0.26910.50540.50550.19030.39310.24480.1780.3326-0.01160.188713.5653-48.036530.7446
348.79524.4296-0.25343.63670.5572.86560.20620.5744-0.6755-0.24230.1142-0.58170.540.3047-0.32040.40110.18080.09830.1254-0.03980.239810.2977-60.239935.1435
355.57783.4068-0.25492.6505-0.06711.16640.01480.3882-0.7988-0.37430.0377-0.63180.31990.1703-0.05250.40870.21290.11530.1687-0.05690.305511.252-55.396237.9744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 24
2X-RAY DIFFRACTION2A25 - 48
3X-RAY DIFFRACTION3A49 - 73
4X-RAY DIFFRACTION4A74 - 85
5X-RAY DIFFRACTION5A86 - 111
6X-RAY DIFFRACTION6A112 - 170
7X-RAY DIFFRACTION7B2 - 23
8X-RAY DIFFRACTION8B24 - 52
9X-RAY DIFFRACTION9B53 - 85
10X-RAY DIFFRACTION10B86 - 108
11X-RAY DIFFRACTION11B109 - 170
12X-RAY DIFFRACTION12C2 - 23
13X-RAY DIFFRACTION13C24 - 53
14X-RAY DIFFRACTION14C54 - 88
15X-RAY DIFFRACTION15C89 - 103
16X-RAY DIFFRACTION16C104 - 139
17X-RAY DIFFRACTION17C140 - 171
18X-RAY DIFFRACTION18D2 - 22
19X-RAY DIFFRACTION19D23 - 34
20X-RAY DIFFRACTION20D35 - 52
21X-RAY DIFFRACTION21D53 - 87
22X-RAY DIFFRACTION22D88 - 128
23X-RAY DIFFRACTION23D129 - 173
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30X-RAY DIFFRACTION30F2 - 42
31X-RAY DIFFRACTION31F43 - 71
32X-RAY DIFFRACTION32F72 - 85
33X-RAY DIFFRACTION33F86 - 125
34X-RAY DIFFRACTION34F126 - 149
35X-RAY DIFFRACTION35F150 - 173

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