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- PDB-6cy6: Crystal structure of spermidine/spermine N-acetyltransferase SpeG... -

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Basic information

Entry
Database: PDB / ID: 6cy6
TitleCrystal structure of spermidine/spermine N-acetyltransferase SpeG from Escherichia coli in complex with tris(hydroxymethyl)aminomethane.
ComponentsSpermidine N(1)-acetyltransferase
KeywordsTRANSFERASE / SpeG / spermidine / GNAT / N-acetyltransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


diamine N-acetyltransferase complex / spermidine catabolic process / spermine catabolic process / diamine N-acetyltransferase / polyamine catabolic process / diamine N-acetyltransferase activity / coenzyme A metabolic process / magnesium ion binding / protein-containing complex / identical protein binding
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Analysis of crystalline and solution states of ligand-free spermidine N-acetyltransferase (SpeG) from Escherichia coli.
Authors: Filippova, E.V. / Weigand, S. / Kiryukhina, O. / Wolfe, A.J. / Anderson, W.F.
History
DepositionApr 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spermidine N(1)-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,05817
Polymers21,9201
Non-polymers1,13816
Water1,892105
1
A: Spermidine N(1)-acetyltransferase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)276,694204
Polymers263,04012
Non-polymers13,654192
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_775-x+2,-y+2,z1
crystal symmetry operation5_565y,-x+y+1,z1
crystal symmetry operation6_655x-y+1,x,z1
crystal symmetry operation7_558y,x,-z+31
crystal symmetry operation8_678x-y+1,-y+2,-z+31
crystal symmetry operation9_768-x+2,-x+y+1,-z+31
crystal symmetry operation10_778-y+2,-x+2,-z+31
crystal symmetry operation11_658-x+y+1,y,-z+31
crystal symmetry operation12_568x,x-y+1,-z+31
Buried area75860 Å2
ΔGint-1536 kcal/mol
Surface area78120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.499, 107.499, 65.021
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21920.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: speG, b1584, JW1576 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: P0A951, diamine N-acetyltransferase

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Non-polymers , 6 types, 121 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.47 Å3/Da / Density % sol: 50.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium phosphate monobasic, 0.1 M Tris, 50% v/v MPD

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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: Nov 15, 2016 / Details: Beryllium Lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 22903 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.048 / Rmerge(I) obs: 0.048 / Net I/σ(I): 51.1
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 13 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1109 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
BLU-MAXdata collection
HKL-3000data scaling
HKL-3000data reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R9M

4r9m


Resolution: 1.75→93.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.547 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20067 1144 5 %RANDOM
Rwork0.15352 ---
obs0.15587 21759 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---1.02 Å2
Refinement stepCycle: 1 / Resolution: 1.75→93.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 65 105 1592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191573
X-RAY DIFFRACTIONr_bond_other_d0.0010.021469
X-RAY DIFFRACTIONr_angle_refined_deg2.0981.9772133
X-RAY DIFFRACTIONr_angle_other_deg1.00533381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0255182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24623.44887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.26615274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.061513
X-RAY DIFFRACTIONr_chiral_restr0.1320.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.021736
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02345
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_it2.2372.035711
X-RAY DIFFRACTIONr_mcbond_other2.2252.026709
X-RAY DIFFRACTIONr_mcangle_it3.1483.028898
X-RAY DIFFRACTIONr_mcangle_other3.1463.034899
X-RAY DIFFRACTIONr_scbond_it4.3172.737862
X-RAY DIFFRACTIONr_scbond_other4.282.724859
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2043.9091230
X-RAY DIFFRACTIONr_long_range_B_refined7.60725.4021715
X-RAY DIFFRACTIONr_long_range_B_other7.52625.121702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.749→1.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 88 -
Rwork0.19 1576 -
obs--99.46 %
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)
14.4601-1.10690.02441.92140.45491.27160.00030.28860.0823-0.2386-0.01840.10210.0522-0.07160.0180.0517-0.0227-0.01450.03770.00190.01869.344273.674375.0326
24.2768-1.54481.02940.8942-0.02490.6119-0.0604-0.0758-0.33160.01370.02350.2149-0.0197-0.02470.03690.05350.00690.00080.02930.01560.114762.399965.327386.5084
31.14720.12250.13710.7625-0.28590.4026-0.03910.0892-0.0342-0.11020.04330.00840.09240.0317-0.00430.0745-0.0002-0.01560.0353-0.02090.023375.026267.465183.4306
43.8351.0702-0.90190.7564-0.35480.574-0.08240.0736-0.4012-0.0570.0119-0.1421-0.019-0.06260.07050.05040.0296-0.01150.0234-0.02010.066673.233752.762388.9859
52.1502-1.58970.72763.8788-2.12071.89170.15380.2428-0.1749-0.1305-0.2491-0.5750.10720.24270.09530.07270.0483-0.00810.1106-0.03640.293791.409563.508988.0334
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 24
2X-RAY DIFFRACTION2A25 - 38
3X-RAY DIFFRACTION3A39 - 134
4X-RAY DIFFRACTION4A135 - 162
5X-RAY DIFFRACTION5A163 - 173

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