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- PDB-1s7f: RimL- Ribosomal L7/L12 alpha-N-protein acetyltransferase crystal ... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1s7f
TitleRimL- Ribosomal L7/L12 alpha-N-protein acetyltransferase crystal form I (apo)
Componentsacetyl transferase
KeywordsTRANSFERASE / acetyltransferase / GNAT / alpha-N-protein acetyltransferase / Coenzyme A / L7/L12
Function / homology
Function and homology information


protein N-terminal-serine acetyltransferase activity / protein-N-terminal-alanine acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm
Similarity search - Function
: / Acetyltransferase (GNAT) domain / 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
MALONIC ACID / Acetyl transferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2 Å
AuthorsVetting, M.W. / de Carvalho, L.P. / Roderick, S.L. / Blanchard, J.S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: A novel dimeric structure of the RimL Nalpha-acetyltransferase from Salmonella typhimurium.
Authors: Vetting, M.W. / de Carvalho, L.P. / Roderick, S.L. / Blanchard, J.S.
History
DepositionJan 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: acetyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9413
Polymers22,8021
Non-polymers1402
Water1,856103
1
A: acetyl transferase
hetero molecules

A: acetyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8836
Polymers45,6042
Non-polymers2794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)68.400, 68.400, 89.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations -1 0 0 0 1 0 0 0 -1 68.4 0 0

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Components

#1: Protein acetyl transferase / Acetylating enzyme for N-terminal of ribosomal protein L7/L12 / RIML


Mass: 22801.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: RimL / Plasmid: pet28a+ / Production host: Escherichia coli (E. coli)
References: UniProt: Q8ZPC0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion under oil / pH: 7.8
Details: triethanolamine, ammonium sulfate, sodium malonate, pH 7.8, vapor diffusion under oil, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 13, 2002 / Details: MSC Blue Confocal
RadiationMonochromator: MSC Blue Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 14015 / Num. obs: 14015 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 35.5 Å2 / Rsym value: 0.032 / Net I/σ(I): 18.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rsym value: 0.154 / % possible all: 83.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 695 -Random
Rwork0.195 ---
all0.195 13920 --
obs0.195 13920 93 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 8 103 1566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_bond_d0.022
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree: 0.326 / Rfactor Rwork: 0.303

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