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

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Basic information

Entry
Database: PDB / ID: 8rmz
TitleApoform of spermine/spermidine acetyl transferase (AtSSAT) from A. thaliana
ComponentsGCN5-related N-acetyltransferase 8
KeywordsTRANSFERASE / 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
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
GCN5-related N-acetyltransferase 8
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.739 Å
AuthorsMorera, S. / Briozzo, P.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: To Be Published
Title: Not defined yet, more later
Authors: Morera, S. / Briozzo, P.
History
DepositionJan 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GCN5-related N-acetyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8426
Polymers26,4631
Non-polymers3785
Water1,58588
1
A: GCN5-related N-acetyltransferase 8
hetero molecules

A: GCN5-related N-acetyltransferase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,68312
Polymers52,9272
Non-polymers75710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area8770 Å2
ΔGint-89 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.24, 101.24, 48.905
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

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Components

#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 interestN
Has protein modificationN

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

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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, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 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!
CC1/2: 0.999 / CC1/2 anomalous: -0.402 / Rmerge(I) obs: 0.1072 / Rpim(I) all: 0.0214 / Rrim(I) all: 0.1094 / AbsDiff over sigma anomalous: 0.581 / Baniso tensor eigenvalue 1: 0 Å2 / Baniso tensor eigenvalue 2: 0 Å2 / Baniso tensor eigenvalue 3: 21.35 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso 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 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
5.263-71.58723.930.055834.312603226032108810880.999-0.4790.01170.05710.36110010010010010014.49100
4.126-5.26225.740.066935.72800928009108810880.999-0.4570.01330.06830.37610010010010010014.49100
3.584-4.12625.060.083532.752729327293108910890.997-0.4070.0170.08520.45210010010010010013.86100
3.242-3.58326.850.098631.142921129211108810880.998-0.4060.01920.10050.44210010010010010014.67100
3.002-3.24227.360.121726.732977229772108810880.998-0.4380.02370.12410.51210010010010010014.86100
2.817-3.00227.760.146622.593020230202108810880.998-0.4750.02810.14930.52810010010010010014.97100
2.672-2.81725.260.187417.742748727487108810880.997-0.370.03790.19130.61610010010010010013.58100
2.552-2.67226.560.235714.982892428924108910890.996-0.1730.04670.24040.699.999.999.999.999.914.2199.9
2.45-2.55227.180.296912.32957229572108810880.995-0.1010.05790.30260.64210010010010010014.49100
2.363-2.4526.70.355810.462905429054108810880.988-0.1950.070.36270.63910010010010010014.2100
2.288-2.36325.010.44318.32720827208108810880.986-0.1320.08980.45220.63810010010010010013.28100
2.22-2.28826.530.52817.422886028860108810880.986-0.0810.10430.53850.64110010010010010014.04100
2.16-2.2226.950.70155.892934929349108910890.972-0.0820.13720.71490.64510010010010010014.3100
2.105-2.1627.370.88434.812977529775108810880.962-0.1280.17170.9010.60998.998.498.998.498.914.4398.4
2.054-2.10527.531.00154.382995629956108810880.9530.0130.19391.02030.6495.194.595.194.595.114.4894.5
2.002-2.05427.651.08934.023008230082108810880.9390.0090.21031.10960.63890.690.690.685.98714.5590.6
1.95-2.00227.531.30293.372995829958108810880.911-0.0640.25221.32730.63588.188.288.176.777.114.4188.2
1.897-1.9526.421.79272.432877428774108910890.8470.0190.35481.82790.65488.88988.867.667.713.989
1.84-1.89723.682.44061.772576125761108810880.720.0020.51122.49420.63189.489.689.45756.812.4289.6
1.739-1.8422.743.12261.362473624736108810880.578-0.0170.66753.1940.61766.564.866.526.726.411.9664.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROC1.0.5 20221121data processing
autoPROCJun 30, 2023data processing
Aimless0.7.7data scaling
autoPROC2.3.90data processing
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.739→18.8 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.189 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 1113 -RANDOM
Rwork0.2076 ---
obs0.2085 21733 81.5 %-
Displacement parametersBiso mean: 47.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.8103 Å20 Å20 Å2
2---0.8103 Å20 Å2
3---1.6206 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.739→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 0 22 88 1830
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093484HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.026273HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d984SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes529HARMONIC5
X-RAY DIFFRACTIONt_it3484HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion225SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2925SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4
X-RAY DIFFRACTIONt_other_torsion15.74
LS refinement shellResolution: 1.74→1.8 Å
RfactorNum. reflection% reflection
Rfree0.3405 24 -
Rwork0.2751 --
obs0.2787 435 15.58 %
Refinement TLS params.Origin x: -1.1177 Å / Origin y: 20.5283 Å / Origin z: -9.6447 Å
111213212223313233
T-0.2786 Å20.0188 Å20.0526 Å2--0.3665 Å20.0073 Å2---0.2773 Å2
L1.3665 °2-0.0101 °20.5416 °2-0.7972 °2-0.1085 °2--0.9734 °2
S0.0043 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 groupSelection details: { A|* }

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