PDB-8rmz: Apoform of spermine/spermidine acetyl transferase (AtSSAT) from A...

ID or keywords:

Entry

Database: PDB / ID: 8rmz

Title

Apoform of spermine/spermidine acetyl transferase (AtSSAT) from A. thaliana

Components

GCN5-related N-acetyltransferase 8

Keywords

TRANSFERASE / enzyme

Function / homology

Function and homology information

protein-N-terminal amino-acid acetyltransferase activity / N-acetyltransferase activity / protein-lysine-acetyltransferase activity / histone acetyltransferase / nucleus / cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.739 Å

Authors

Morera, S. / Briozzo, P.

Funding support

France, 1items

Citation

Journal: To Be Published
Title: Not defined yet, more later
Authors: Morera, S. / Briozzo, P.

History

Deposition	Jan 9, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8rmz.cif.gz	140.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8rmz.ent.gz	110.6 KB	Display	PDB format
PDBx/mmJSON format	8rmz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8rmz_validation.pdf.gz	452.5 KB	Display	wwPDB validaton report
Full document	8rmz_full_validation.pdf.gz	452.6 KB	Display
Data in XML	8rmz_validation.xml.gz	12.2 KB	Display
Data in CIF	8rmz_validation.cif.gz	15.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rm/8rmz ftp://data.pdbj.org/pub/pdb/validation_reports/rm/8rmz	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4) #122 - Feb 2010 Enhanceosome similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (4) #67 - Jul 2005 TATA-Binding Protein similarity (1)

Deposited unit

A: GCN5-related N-acetyltransferase 8

hetero molecules

26.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GCN5-related N-acetyltransferase 8

hetero molecules

A: GCN5-related N-acetyltransferase 8

hetero molecules

defined by author&software
Evidence: gel filtration
53.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.24, 101.24, 48.905
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-427- HOH

#1: Protein	GCN5-related N-acetyltransferase 8 / Probable acetyltransferase NATA1-like Mass: 26463.379 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GNAT8, At2g39020, T7F6.19 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9ZV06, histone acetyltransferase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.05 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: PEG 4000, Ammonium Sulfate, Na citrate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 2 / Wavelength: 0.99187 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.99187 Å / Relative weight: 1

Reflection

Resolution: 1.739→71.587 Å / Num. obs: 21764 / % possible obs: 94.8 % / Redundancy: 26.19 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC_1/2: 0.999 / CC_1/2 anomalous: -0.402 / R_merge(I) obs: 0.1072 / R_pim(I) all: 0.0214 / R_rim(I) all: 0.1094 / AbsDiff over sigma anomalous: 0.581 / B_aniso tensor eigenvalue 1: 0 Å² / B_aniso tensor eigenvalue 2: 0 Å² / B_aniso tensor eigenvalue 3: 21.35 Å² / B_aniso tensor eigenvector 1 ortho1: 1 / B_aniso tensor eigenvector 1 ortho2: 0 / B_aniso tensor eigenvector 1 ortho3: 0 / B_aniso tensor eigenvector 2 ortho1: 0 / B_aniso tensor eigenvector 2 ortho2: 1 / B_aniso tensor eigenvector 2 ortho3: 0 / B_aniso tensor eigenvector 3 ortho1: 0 / B_aniso tensor eigenvector 3 ortho2: 0 / B_aniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 1.73 Å / Aniso diffraction limit 2: 1.73 Å / Aniso diffraction limit 3: 2.05 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 14.12 / Num. measured all: 570015 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 94.8 / % possible ellipsoidal: 94.8 / % possible ellipsoidal anomalous: 94.8 / % possible spherical: 81.6 / % possible spherical anomalous: 80.9 / Redundancy anomalous: 14.07 / Signal type: local

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	CC_1/2 anomalous	R_pim(I) all	R_rim(I) all	AbsDiff over sigma anomalous	% possible anomalous	% possible ellipsoidal	% possible ellipsoidal anomalous	% possible spherical	% possible spherical anomalous	Redundancy anomalous	% possible all
5.263-71.587	23.93	0.0558	34.31	26032	26032	1088	1088	0.999	-0.479	0.0117	0.0571	0.361	100	100	100	100	100	14.49	100
4.126-5.262	25.74	0.0669	35.7	28009	28009	1088	1088	0.999	-0.457	0.0133	0.0683	0.376	100	100	100	100	100	14.49	100
3.584-4.126	25.06	0.0835	32.75	27293	27293	1089	1089	0.997	-0.407	0.017	0.0852	0.452	100	100	100	100	100	13.86	100
3.242-3.583	26.85	0.0986	31.14	29211	29211	1088	1088	0.998	-0.406	0.0192	0.1005	0.442	100	100	100	100	100	14.67	100
3.002-3.242	27.36	0.1217	26.73	29772	29772	1088	1088	0.998	-0.438	0.0237	0.1241	0.512	100	100	100	100	100	14.86	100
2.817-3.002	27.76	0.1466	22.59	30202	30202	1088	1088	0.998	-0.475	0.0281	0.1493	0.528	100	100	100	100	100	14.97	100
2.672-2.817	25.26	0.1874	17.74	27487	27487	1088	1088	0.997	-0.37	0.0379	0.1913	0.616	100	100	100	100	100	13.58	100
2.552-2.672	26.56	0.2357	14.98	28924	28924	1089	1089	0.996	-0.173	0.0467	0.2404	0.6	99.9	99.9	99.9	99.9	99.9	14.21	99.9
2.45-2.552	27.18	0.2969	12.3	29572	29572	1088	1088	0.995	-0.101	0.0579	0.3026	0.642	100	100	100	100	100	14.49	100
2.363-2.45	26.7	0.3558	10.46	29054	29054	1088	1088	0.988	-0.195	0.07	0.3627	0.639	100	100	100	100	100	14.2	100
2.288-2.363	25.01	0.4431	8.3	27208	27208	1088	1088	0.986	-0.132	0.0898	0.4522	0.638	100	100	100	100	100	13.28	100
2.22-2.288	26.53	0.5281	7.42	28860	28860	1088	1088	0.986	-0.081	0.1043	0.5385	0.641	100	100	100	100	100	14.04	100
2.16-2.22	26.95	0.7015	5.89	29349	29349	1089	1089	0.972	-0.082	0.1372	0.7149	0.645	100	100	100	100	100	14.3	100
2.105-2.16	27.37	0.8843	4.81	29775	29775	1088	1088	0.962	-0.128	0.1717	0.901	0.609	98.9	98.4	98.9	98.4	98.9	14.43	98.4
2.054-2.105	27.53	1.0015	4.38	29956	29956	1088	1088	0.953	0.013	0.1939	1.0203	0.64	95.1	94.5	95.1	94.5	95.1	14.48	94.5
2.002-2.054	27.65	1.0893	4.02	30082	30082	1088	1088	0.939	0.009	0.2103	1.1096	0.638	90.6	90.6	90.6	85.9	87	14.55	90.6
1.95-2.002	27.53	1.3029	3.37	29958	29958	1088	1088	0.911	-0.064	0.2522	1.3273	0.635	88.1	88.2	88.1	76.7	77.1	14.41	88.2
1.897-1.95	26.42	1.7927	2.43	28774	28774	1089	1089	0.847	0.019	0.3548	1.8279	0.654	88.8	89	88.8	67.6	67.7	13.9	89
1.84-1.897	23.68	2.4406	1.77	25761	25761	1088	1088	0.72	0.002	0.5112	2.4942	0.631	89.4	89.6	89.4	57	56.8	12.42	89.6
1.739-1.84	22.74	3.1226	1.36	24736	24736	1088	1088	0.578	-0.017	0.6675	3.194	0.617	66.5	64.8	66.5	26.7	26.4	11.96	64.8

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Processing

Software

Name	Version	Classification
BUSTER	2.10.4	refinement
autoPROC	1.0.5 20221121	data processing
autoPROC	Jun 30, 2023	data processing
Aimless	0.7.7	data scaling
autoPROC	2.3.90	data processing
autoPROC		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.739→18.8 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.948 / SU R Cruickshank DPI: 0.189 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.141 / SU R_free Blow DPI: 0.123 / SU R_free Cruickshank DPI: 0.122

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2256	1113	-	RANDOM
R_work	0.2076	-	-	-
obs	0.2085	21733	81.5 %	-

Displacement parameters

B_iso mean: 47.41 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.8103 Å²	0 Å²	0 Å²
2-	-	-0.8103 Å²	0 Å²
3-	-	-	1.6206 Å²

Refine analyze

Luzzati coordinate error obs: 0.25 Å

Refinement step

Cycle: LAST / Resolution: 1.739→18.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1720	0	22	88	1830

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.009	3484	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.02	6273	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		984	SINUSOIDAL	2
X-RAY DIFFRACTION	t_gen_planes		529	HARMONIC	5
X-RAY DIFFRACTION	t_it		3484	HARMONIC	10
X-RAY DIFFRACTION	t_chiral_improper_torsion		225	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_ideal_dist_contact		2925	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_omega_torsion	4
X-RAY DIFFRACTION	t_other_torsion	15.74

LS refinement shell

Resolution: 1.74→1.8 Å

	R_factor	Num. reflection	% reflection
R_free	0.3405	24	-
R_work	0.2751	-	-
obs	0.2787	435	15.58 %

Refinement TLS params.

Origin x: -1.1177 Å / Origin y: 20.5283 Å / Origin z: -9.6447 Å

	11	12	13	21	22	23	31	32	33
T	-0.2786 Å²	0.0188 Å²	0.0526 Å²	-	-0.3665 Å²	0.0073 Å²	-	-	-0.2773 Å²
L	1.3665 °²	-0.0101 °²	0.5416 °²	-	0.7972 °²	-0.1085 °²	-	-	0.9734 °²
S	0.0043 Å °	0.0127 Å °	-0.2406 Å °	0.0127 Å °	0.002 Å °	0.0098 Å °	-0.2406 Å °	0.0098 Å °	-0.0063 Å °

Refinement TLS group

Selection details: { A|* }

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