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- PDB-6d72: Crystal structure of spermidine/spermine N-acetyltransferase SpeG... -

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Basic information

Entry
Database: PDB / ID: 6d72
TitleCrystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis in complex with calcium ions.
ComponentsSpermidine N1-acetyltransferase
KeywordsTRANSFERASE / SpeG / polyamine / GNAT / N-acetyltransferase / 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
MALONATE ION / DI(HYDROXYETHYL)ETHER / Spermidine acetyltransferase / Spermidine acetyltransferase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsFilippova, E.V. / Minasov, G. / Kiryukhina, O. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / 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: To Be Published
Title: Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis in complex with calcium ions.
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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_conn_type / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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 / _struct_conn_type.id / _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)65,71115
Polymers64,6643
Non-polymers1,04712
Water3,369187
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)262,84360
Polymers258,65512
Non-polymers4,18748
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 area49420 Å2
ΔGint-98 kcal/mol
Surface area82340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.761, 120.804, 123.330
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
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAA6 - 1749 - 177
21SERSERLYSLYSBB6 - 1749 - 177
12SERSERTYRTYRAA6 - 1739 - 176
22SERSERTYRTYRCC6 - 1739 - 176
13ALAALATYRTYRBB0 - 1733 - 176
23ALAALATYRTYRCC0 - 1733 - 176

NCS ensembles :
ID
1
2
3

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Imidazole, 14% (w/v) PEG10000

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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 MX300-HS / 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: 2.17→30 Å / Num. obs: 40132 / % possible obs: 99.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 23.3
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2006 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
BLU-MAXdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WIF

5wif


Resolution: 2.17→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 10.568 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.165 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21235 1952 4.9 %RANDOM
Rwork0.18207 ---
obs0.1835 38176 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 55.287 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---2.85 Å20 Å2
3---2.24 Å2
Refinement stepCycle: 1 / Resolution: 2.17→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4354 0 66 187 4607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194602
X-RAY DIFFRACTIONr_bond_other_d0.0020.024219
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9636176
X-RAY DIFFRACTIONr_angle_other_deg1.00439766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0955533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97723.837245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94815826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4191532
X-RAY DIFFRACTIONr_chiral_restr0.1070.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025104
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02988
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_it2.4394.0862129
X-RAY DIFFRACTIONr_mcbond_other2.3754.0782122
X-RAY DIFFRACTIONr_mcangle_it3.5376.12659
X-RAY DIFFRACTIONr_mcangle_other3.5376.1022660
X-RAY DIFFRACTIONr_scbond_it3.2794.4362473
X-RAY DIFFRACTIONr_scbond_other3.2784.4362474
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3836.5043518
X-RAY DIFFRACTIONr_long_range_B_refined6.27946.4334933
X-RAY DIFFRACTIONr_long_range_B_other6.26246.1324897
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 / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110900.07
12B110900.07
21A109800.08
22C109800.08
31B112560.09
32C112560.09
LS refinement shellResolution: 2.17→2.226 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 127 -
Rwork0.275 2812 -
obs--98.66 %
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)
13.18711.35182.50285.3059-1.32454.8893-0.1428-0.00660.2725-0.20110.15310.58650.1274-0.2117-0.01030.0313-0.00890.00050.1058-0.00190.265-21.8009130.037524.0072
22.0650.7820.68762.3418-0.57071.7519-0.0288-0.12680.24010.09440.0180.3951-0.0752-0.05010.01080.0108-0.00840.02450.0644-0.04640.1155-13.58131.892428.708
36.20752.2353-1.02577.4023-4.00246.4102-0.0955-0.47250.35580.88570.36930.6652-0.4234-0.3897-0.27380.18590.01020.13970.1748-0.07360.1521-12.6627142.81242.5489
40.27650.6305-0.19586.7741-3.8433.68660.0274-0.22680.09940.6410.01350.0995-0.3636-0.2705-0.04090.1210.010.04910.2633-0.1050.0966-8.1691139.796439.0722
50.2742-0.3491-0.5210.4550.66950.9938-0.157-0.1480.00420.20090.2024-0.06380.30350.2839-0.04540.1926-0.0404-0.08580.25330.01870.387532.0993153.046427.9198
62.15610.0758-0.73812.8877-0.59721.6644-0.0065-0.2119-0.1941-0.1342-0.1962-0.20350.05210.13650.20270.0107-0.0090.01610.12130.010.070115.5974133.310720.4028
70.9706-0.0601-0.85331.55830.04981.9535-0.0111-0.11450.08190.181-0.0605-0.0738-0.11550.29680.07160.0487-0.055-0.01510.1487-0.04780.081413.4063145.858826.673
81.27730.64130.02785.8701-1.69391.25060.0468-0.19460.19790.573-0.0748-0.1222-0.21910.09240.02790.1162-0.0604-0.01720.1951-0.0960.07969.9839145.872438.071
912.52316.4825-6.28113.3635-3.28445.9542-0.1612-0.3891-0.4141-0.0406-0.264-0.201-0.42180.02530.42520.2543-0.01820.16270.25380.01750.30730.8104160.5153-18.362
102.2695-0.68250.11071.163-0.3552.8540.0288-0.04540.2348-0.0801-0.0087-0.0422-0.20040.3879-0.020.0343-0.04010.0170.0665-0.01720.05614.6517150.0758-4.1095
111.25050.4102-0.87491.6996-1.32388.12720.0359-0.03250.28430.0457-0.0905-0.0677-0.95140.39790.05460.1927-0.07520.01020.03410.00620.14779.8683166.51872.1395
126.29910.6312-0.21970.39670.74852.35140.00210.8190.6368-0.1203-0.02480.0073-0.2723-0.24920.02270.12460.010.02870.1580.11970.159410.2721165.2547-19.2283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 25
2X-RAY DIFFRACTION2A26 - 121
3X-RAY DIFFRACTION3A122 - 145
4X-RAY DIFFRACTION4A146 - 175
5X-RAY DIFFRACTION5B0 - 7
6X-RAY DIFFRACTION6B8 - 66
7X-RAY DIFFRACTION7B67 - 123
8X-RAY DIFFRACTION8B124 - 175
9X-RAY DIFFRACTION9C-2 - 8
10X-RAY DIFFRACTION10C9 - 121
11X-RAY DIFFRACTION11C122 - 164
12X-RAY DIFFRACTION12C165 - 174

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