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- PDB-5wif: Crystal structure of spermidine/spermine N-acetyltransferase SpeG... -

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Basic information

Entry
Database: PDB / ID: 5wif
TitleCrystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis
ComponentsSpermidine N1-acetyltransferase
KeywordsTRANSFERASE / polyamines / GNAT / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


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
BORIC ACID / : / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Spermidine acetyltransferase / Spermidine acetyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Shatsman, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis
Authors: Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Shatsman, S. / Anderson, W.F.
History
DepositionJul 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 4, 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 / struct_ncs_dom_lim
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_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_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_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.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_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0497
Polymers64,6643
Non-polymers3854
Water72140
1
A: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
hetero molecules

A: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
hetero molecules

A: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
hetero molecules

A: Spermidine N1-acetyltransferase
B: Spermidine N1-acetyltransferase
C: Spermidine N1-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,19728
Polymers258,65512
Non-polymers1,54116
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area36680 Å2
ΔGint-46 kcal/mol
Surface area87040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.596, 120.114, 122.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13A
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRBB6 - 1739 - 176
21TYRTYRAA6 - 1739 - 176
12LYSLYSBB-1 - 1742 - 177
22LYSLYSCC-1 - 1742 - 177
13TYRTYRAA6 - 1739 - 176
23TYRTYRCC6 - 1739 - 176

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Spermidine N1-acetyltransferase / Spermidine acetyltransferase


Mass: 21554.619 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: speG, y1405, YP_2698 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q0WD68, UniProt: A0A5P8YIA2*PLUS

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Non-polymers , 5 types, 44 molecules

#2: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Triethylene glycol dimethyl ether


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-BO3 / BORIC ACID / Boric acid


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M MIB buffer, 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 11, 2017 / 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: 2.5→30 Å / Num. obs: 26195 / % possible obs: 99.7 % / Redundancy: 5.7 % / CC1/2: 0.9 / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.6
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 1292 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CNP

5cnp


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 21.766 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.367 / ESU R Free: 0.258 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24189 1276 4.9 %RANDOM
Rwork0.18841 ---
obs0.19087 24919 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.548 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å2-0 Å20 Å2
2---4 Å2-0 Å2
3---5.22 Å2
Refinement stepCycle: 1 / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 22 40 4342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194416
X-RAY DIFFRACTIONr_bond_other_d0.0020.024106
X-RAY DIFFRACTIONr_angle_refined_deg1.9551.9585935
X-RAY DIFFRACTIONr_angle_other_deg1.10239512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.935510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4623.691233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30715806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7321530
X-RAY DIFFRACTIONr_chiral_restr0.1230.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024829
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02957
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_it3.8655.5212055
X-RAY DIFFRACTIONr_mcbond_other3.865.5212054
X-RAY DIFFRACTIONr_mcangle_it5.6298.2682560
X-RAY DIFFRACTIONr_mcangle_other5.6298.2692561
X-RAY DIFFRACTIONr_scbond_it4.3335.8942361
X-RAY DIFFRACTIONr_scbond_other4.3325.8942361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4868.6733376
X-RAY DIFFRACTIONr_long_range_B_refined8.48260.7714664
X-RAY DIFFRACTIONr_long_range_B_other8.48260.7884665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11B10746
12A10746
21B11040
22C11040
31A10788
32C10788
LS refinement shellResolution: 2.506→2.571 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 87 -
Rwork0.333 1716 -
obs--94.99 %
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)
13.7991.92171.355.5943-0.79758.0275-0.18360.1995-0.1855-0.1730.25940.68170.3777-0.5214-0.07580.0541-0.0149-0.00470.1034-0.0320.2259-22.0144128.051724.1404
26.14783.43390.30429.92810.64053.8916-0.2465-0.03580.4411-0.73730.44690.0476-0.01690.1517-0.20040.074-0.037-0.02270.0326-0.01680.0656-11.9605134.933917.0785
36.5144-0.47860.66732.48551.74064.2932-0.1261-0.4649-0.07740.02190.01840.52750.146-0.04680.10770.05850.02680.00580.0451-0.02170.2823-17.4373127.834828.1
46.3996-0.72072.06222.722-1.46581.4848-0.0939-0.39710.23060.5428-0.03360.3396-0.4027-0.13190.12750.27160.05150.01040.1533-0.10150.3105-14.856131.752235.1882
51.30460.20040.14947.0024-2.70483.04950.0144-0.18060.06171.01440.1110.3726-0.482-0.0495-0.12540.15630.00310.06640.0841-0.05060.066-9.2678139.640538.9015
615.9387-4.1017-3.40183.3345-1.72563.6947-0.3606-1.2772-0.14960.57290.74460.4026-0.4734-0.2003-0.3840.2790.01610.10050.24750.05230.0817-12.5191124.809648.6967
719.3652-8.7366-16.59933.94197.488914.2303-0.2444-0.4032-0.04550.10290.18340.02990.21490.34790.0610.1857-0.0581-0.11430.2750.03330.452933.2405154.364828.487
82.7716-1.3298-0.47352.87213.57728.6453-0.0022-0.1719-0.0985-0.3595-0.1116-0.31990.20850.21260.11380.27720.05560.11830.36990.11850.328921.4953136.236419.5676
93.4094-0.2849-2.04113.80490.06771.80080.0446-0.3306-0.103-0.0747-0.2005-0.16920.08760.22850.15580.0438-0.00350.00280.12420.03950.038912.8045136.337222.6227
106.8933-3.43411.21123.4264-0.5191.7443-0.0527-0.12980.12830.40020.006-0.1066-0.27220.23180.04670.1806-0.1075-0.06910.14760.02410.090116.7266149.293626.6208
112.04590.9807-0.40298.8707-2.45791.71840.1045-0.28840.13550.9838-0.11010.0005-0.28990.07750.00560.2033-0.0554-0.02670.1088-0.02440.02359.2942142.046239.4188
126.91663.88311.26564.46375.27349.3535-0.43160.31990.7898-0.26830.16790.4954-0.14940.03350.26370.1288-0.036-0.06260.04350.02940.258611.1453160.261729.0264
1310.80140.8448-3.09980.3865-1.27924.4332-0.02870.69080.27790.14110.0206-0.051-0.5431-0.28710.00810.12760.03850.07870.22140.09110.2207-33.6195162.368919.3104
144.0553.0834-0.76299.08112.32394.5903-0.02110.1631-0.11330.0991-0.0347-0.14980.3333-0.73770.05580.0445-0.01680.02430.2642-0.0060.0808-21.7041145.02383.9423
153.35131.7147-0.79871.49260.31994.4757-0.06070.26910.01990.0490.0019-0.10120.2545-0.43740.05880.0678-0.0084-0.01010.07630.00660.0573-12.0643146.93872.7563
166.79842.06393.4761.57561.85424.3164-0.15150.0560.3749-0.0214-0.03080.3349-0.6322-0.25710.18220.19280.09680.0450.10760.01520.1281-17.3476157.36828.8997
171.34760.1589-0.5981.480.955610.48860.05230.09880.41780.08650.03890.0578-0.8839-0.2659-0.09120.18860.0618-0.0080.0260.02050.1489-9.835165.468-1.5909
1812.92021.5567-3.17796.44120.14510.64420.4856-2.28370.52350.5687-0.40620.0985-0.90840.1944-0.07930.32610.00120.11060.4901-0.15220.2796-10.5432165.086319.0685
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 23
2X-RAY DIFFRACTION2A24 - 52
3X-RAY DIFFRACTION3A53 - 75
4X-RAY DIFFRACTION4A76 - 109
5X-RAY DIFFRACTION5A110 - 167
6X-RAY DIFFRACTION6A168 - 174
7X-RAY DIFFRACTION7B-1 - 6
8X-RAY DIFFRACTION8B7 - 24
9X-RAY DIFFRACTION9B28 - 93
10X-RAY DIFFRACTION10B94 - 118
11X-RAY DIFFRACTION11B119 - 165
12X-RAY DIFFRACTION12B166 - 175
13X-RAY DIFFRACTION13C0 - 6
14X-RAY DIFFRACTION14C7 - 24
15X-RAY DIFFRACTION15C27 - 86
16X-RAY DIFFRACTION16C87 - 119
17X-RAY DIFFRACTION17C120 - 164
18X-RAY DIFFRACTION18C165 - 174

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