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- PDB-7zhc: Moss spermine/spermidine acetyl transferase (PpSSAT) in complex w... -

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Basic information

Entry
Database: PDB / ID: 7zhc
TitleMoss spermine/spermidine acetyl transferase (PpSSAT) in complex with AcetylCoA and polyethylen glycol
ComponentsN-acetyltransferase domain-containing protein
KeywordsTRANSFERASE / SSAT / COENZYME A / ACYLTRANSFERASE
Function / homology: / N-acetyltransferase activity / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / N-acetyltransferase domain-containing protein
Function and homology information
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.819 Å
AuthorsMorera, S. / Kopecny, D. / Vigouroux, A.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Plant J. / Year: 2023
Title: Biochemical and structural basis of polyamine, lysine and ornithine acetylation catalyzed by spermine/spermidine N-acetyl transferase in moss and maize.
Authors: Belicek, J. / Luptakova, E. / Kopecny, D. / Frommel, J. / Vigouroux, A. / Cavar Zeljkovic, S. / Jagic, F. / Briozzo, P. / Kopecny, D.J. / Tarkowski, P. / Nisler, J. / De Diego, N. / Morera, S. / Kopecna, M.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyltransferase domain-containing protein
B: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1576
Polymers52,2082
Non-polymers1,9504
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-53 kcal/mol
Surface area17140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.108, 97.773, 48.453
Angle α, β, γ (deg.)90.000, 117.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein N-acetyltransferase domain-containing protein


Mass: 26103.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_008003
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2K1KKM6
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 8000, 10% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.99187 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.819→48.89 Å / Num. obs: 23866 / % possible obs: 92.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 35.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.3
Reflection shellResolution: 1.819→2.05 Å / Rmerge(I) obs: 1.138 / Num. unique obs: 1194 / CC1/2: 0.497

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (18-SEP-2020)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BEI

2bei


Resolution: 1.819→48.89 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.183
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1365 5.72 %RANDOM
Rwork0.1994 ---
obs0.2015 23866 66.8 %-
Displacement parametersBiso max: 81.17 Å2 / Biso mean: 42.44 Å2 / Biso min: 19.39 Å2
Baniso -1Baniso -2Baniso -3
1-5.218 Å20 Å2-2.0862 Å2
2---0.9948 Å20 Å2
3----4.2232 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.819→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 121 186 3391
Biso mean--52.92 47.36 -
Num. residues----394
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1135SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes554HARMONIC5
X-RAY DIFFRACTIONt_it3277HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion424SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2869SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3277HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg4458HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion15.85
LS refinement shellResolution: 1.82→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2189 18 3.77 %
Rwork0.2007 460 -
all0.2015 478 -
obs--6.17 %
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)
10.8337-0.81720.95872.4734-0.79243.044-0.0067-0.04120.0789-0.08290.03830.0257-0.2342-0.1679-0.0316-0.2281-0.0227-0.0331-0.29810.0022-0.30345.92687.60041.1507
21.1763-0.61850.75850.7142-0.62722.577-0.04210.04010.04020.0278-0.0003-0.07120.2525-0.0360.0424-0.1892-0.0669-0.0139-0.2809-0.0146-0.294521.1013-8.178312.3153
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 214
2X-RAY DIFFRACTION2{ B|* }B2 - 214

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