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

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Basic information

Entry
Database: PDB / ID: 7zkt
TitleMoss spermine/spermidine acetyl transferase (PpSSAT) in complex with CoA and lysine
ComponentsN-acetyltransferase domain-containing protein
KeywordsTRANSFERASE / Acetylation / moss / SSAT
Function / homologyN-acetyltransferase activity / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / COENZYME A / LYSINE / N-acetyltransferase domain-containing protein
Function and homology information
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsMorera, S. / Kopecny, D. / Vigouroux, A. / Briozzo, P.
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 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 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

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase domain-containing protein
B: N-acetyltransferase domain-containing protein
C: N-acetyltransferase domain-containing protein
D: N-acetyltransferase domain-containing protein
E: N-acetyltransferase domain-containing protein
F: N-acetyltransferase domain-containing protein
G: N-acetyltransferase domain-containing protein
H: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,36746
Polymers208,8318
Non-polymers8,53638
Water12,214678
1
A: N-acetyltransferase domain-containing protein
B: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,55814
Polymers52,2082
Non-polymers2,35012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-99 kcal/mol
Surface area17580 Å2
MethodPISA
2
C: N-acetyltransferase domain-containing protein
D: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,32612
Polymers52,2082
Non-polymers2,11910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-88 kcal/mol
Surface area17170 Å2
MethodPISA
3
E: N-acetyltransferase domain-containing protein
F: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1459
Polymers52,2082
Non-polymers1,9387
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-74 kcal/mol
Surface area17430 Å2
MethodPISA
4
G: N-acetyltransferase domain-containing protein
H: N-acetyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,33711
Polymers52,2082
Non-polymers2,1309
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-93 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.010, 138.430, 129.780
Angle α, β, γ (deg.)90.000, 94.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
N-acetyltransferase domain-containing protein


Mass: 26103.910 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_008003 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K1KKM6

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Non-polymers , 6 types, 716 molecules

#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H15N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.79 Å3/Da / Density % sol: 55.91 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M trisodium citrate pH 5.6, 15 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.06→94.55 Å / Num. obs: 138210 / % possible obs: 98.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 44.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.161 / Net I/σ(I): 7.1
Reflection shellResolution: 2.06→2.291 Å / Rmerge(I) obs: 1.2 / Num. unique obs: 4684 / CC1/2: 0.579

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZHC

7zhc


Resolution: 2.06→94.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.256 / SU Rfree Blow DPI: 0.183 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.202 4303 4.64 %RANDOM
Rwork0.176 ---
obs0.177 92757 65.9 %-
Displacement parametersBiso max: 188.9 Å2 / Biso mean: 55.78 Å2 / Biso min: 19.69 Å2
Baniso -1Baniso -2Baniso -3
1--2.4744 Å20 Å2-2.783 Å2
2--3.1673 Å20 Å2
3----0.6929 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 2.06→94.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12459 0 915 678 14052
Biso mean--60.56 51.61 -
Num. residues----1591
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4553SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2166HARMONIC5
X-RAY DIFFRACTIONt_it13695HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1747SEMIHARMONIC5
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_contact15253SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d13695HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg18692HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion15.66
LS refinement shellResolution: 2.06→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2468 8 5.44 %
Rwork0.2192 139 -
all0.2207 147 -
obs--1.42 %
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)
12.5385-0.28360.5241.24780.14932.18870.05930.1583-0.63150.0329-0.02740.11680.35890.0404-0.0319-0.2949-0.0005-0.0379-0.2001-0.0175-0.134819.8343-7.800534.3453
21.4936-0.00970.09881.38750.461.6135-0.0986-0.05160.20310.18560.08310.0407-0.3255-0.00660.0155-0.1750.0248-0.0561-0.18920.0214-0.253119.730818.197647.9619
31.8601-0.46590.24591.93710.12451.47610.094-0.0348-0.1836-0.1072-0.0028-0.00920.19810.0152-0.0912-0.28180.0199-0.0503-0.1422-0.0197-0.238151.743-3.943915.1053
41.6304-1.37690.11293.4985-0.1461.04680.03270.06550.5792-0.2209-0.0105-0.5805-0.2780.0899-0.0222-0.2788-0.00430.0303-0.2132-0.017-0.117251.801825.234712.89
51.69940.98060.48042.98630.62562.04520.0850.1292-0.029-0.26330.0619-0.4742-0.40540.3629-0.1469-0.1787-0.14370.0535-0.1237-0.0434-0.315749.675172.38352.6554
61.03980.98810.16694.93510.50731.18980.13850.075-0.41860.22780.061-0.9610.19980.2714-0.1995-0.2549-0.001-0.137-0.1911-0.0689-0.132348.011742.948954.7506
71.7865-0.10990.35491.95430.442.40050.029-0.1388-0.17390.05860.02460.15020.1035-0.0849-0.0537-0.20560.021-0.0203-0.17660.0651-0.287222.977750.350115.3733
82.83250.52810.26921.70530.59863.6978-0.0236-0.42890.72530.1164-0.09760.4025-1.1928-0.4240.12120.02480.13490.0069-0.3131-0.0614-0.328120.256976.375928.8478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 214
2X-RAY DIFFRACTION2{ B|* }B2 - 214
3X-RAY DIFFRACTION3{ C|* }C2 - 214
4X-RAY DIFFRACTION4{ D|* }D2 - 214
5X-RAY DIFFRACTION5{ E|* }E2 - 214
6X-RAY DIFFRACTION6{ F|* }F2 - 214
7X-RAY DIFFRACTION7{ G|* }G2 - 214
8X-RAY DIFFRACTION8{ H|* }H4 - 214

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