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- PDB-5ug4: Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 5ug4
TitleStructure of spermidine N-acetyltransferase SpeG from Vibrio cholerae
ComponentsSpermidine N(1)-acetyltransferase
KeywordsTRANSFERASE / SpeG / spermidine / spermine / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
ACETATE ION / ETHANOL / METHANOL / Spermidine N(1)-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Structure of spermidine N-acetyltransferase SpeG from Vibrio cholerae
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_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.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 / _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 N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,84418
Polymers62,1103
Non-polymers73415
Water4,252236
1
A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
hetero molecules

A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
hetero molecules

A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
hetero molecules

A: Spermidine N(1)-acetyltransferase
B: Spermidine N(1)-acetyltransferase
C: Spermidine N(1)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,37772
Polymers248,44112
Non-polymers2,93660
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area44190 Å2
ΔGint-505 kcal/mol
Surface area78100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.884, 134.635, 137.346
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-201-

CA

21B-368-

HOH

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
11ASNASNLEULEUAA2 - 1692 - 169
21ASNASNLEULEUBB2 - 1692 - 169
12SERSERASNASNAA3 - 1703 - 170
22SERSERASNASNCC3 - 1703 - 170
13SERSERLEULEUBB3 - 1693 - 169
23SERSERLEULEUCC3 - 1693 - 169

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Spermidine N(1)-acetyltransferase / SAT / Spermidine/spermine N(1)-acetyltransferase / SSAT


Mass: 20703.385 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Gene: speG, VC_A0947 / Plasmid: MCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) magic / References: UniProt: Q9KL03, diamine N-acetyltransferase

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Non-polymers , 6 types, 251 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#6: Chemical ChemComp-MOH / METHANOL / Methanol


Mass: 32.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4O
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris, 50% MPD, 20% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2011 / Details: beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 36218 / % possible obs: 99.4 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 28.5
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 15 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 8.3 / Num. unique all: 1771 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MI4

4mi4


Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.993 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19986 1812 5 %RANDOM
Rwork0.16929 ---
obs0.17088 34406 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.589 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å20 Å2
2---1.26 Å2-0 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4313 0 34 236 4583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194476
X-RAY DIFFRACTIONr_bond_other_d0.0020.024052
X-RAY DIFFRACTIONr_angle_refined_deg1.9191.9386041
X-RAY DIFFRACTIONr_angle_other_deg1.07939355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70323.852270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73515788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3281538
X-RAY DIFFRACTIONr_chiral_restr0.1190.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025030
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021000
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_it2.0132.9312060
X-RAY DIFFRACTIONr_mcbond_other1.9762.9252055
X-RAY DIFFRACTIONr_mcangle_it2.9434.3652572
X-RAY DIFFRACTIONr_mcangle_other2.9424.3652573
X-RAY DIFFRACTIONr_scbond_it2.7733.3112416
X-RAY DIFFRACTIONr_scbond_other2.7733.3122417
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3074.8423470
X-RAY DIFFRACTIONr_long_range_B_refined5.94234.2765020
X-RAY DIFFRACTIONr_long_range_B_other5.94234.2845021
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)
11A112500.09
12B112500.09
21A113480.09
22C113480.09
31B111520.08
32C111520.08
LS refinement shellResolution: 2.149→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 134 -
Rwork0.175 2265 -
obs--89.62 %
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)
10.6526-0.1386-0.0781.3528-0.04590.6881-0.00220.04820.0215-0.15060.00750.1387-0.0224-0.0425-0.00530.0956-0.0178-0.04020.0353-0.010.0368-13.790353.212-30.9343
20.4864-0.34640.02671.2388-0.16711.36550.0109-0.0233-0.0943-0.0403-0.00940.21410.1218-0.1847-0.00150.0497-0.04590.00220.0546-0.00790.0419-13.815133.5532-3.1962
30.17510.30580.25111.2588-0.10390.9303-0.01720.0838-0.0373-0.0988-0.0196-0.19240.02170.21720.03680.09580.01960.04960.12140.00110.049413.769547.4525-27.5842
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 170
2X-RAY DIFFRACTION2B2 - 170
3X-RAY DIFFRACTION3C3 - 173

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