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- PDB-1s7l: RimL- Ribosomal L7/L12 alpha-N-protein acetyltransferase in compl... -

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Basic information

Entry
Database: PDB / ID: 1s7l
TitleRimL- Ribosomal L7/L12 alpha-N-protein acetyltransferase in complex with Coenzyme A (CoA-Cys134 Disulfide)
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
COENZYME A / Acetyl transferase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: acetyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7763
Polymers20,9131
Non-polymers8642
Water1,15364
1
A: acetyl transferase
hetero molecules

A: acetyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5536
Polymers41,8262
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)92.920, 92.920, 55.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations y, x, -z

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Components

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


Mass: 20912.771 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion under oil / pH: 8
Details: pentaerythritiol ethoxylate 797, triethanolamine, ammonium sulfate, acetylcoenzyme A, DTT, pH 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: Mar 3, 2003 / 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: 2.3→30 Å / Num. all: 10924 / Num. obs: 10924 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 40.3 Å2 / Rsym value: 0.04 / Net I/σ(I): 20.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.9 % / Rsym value: 0.165 / % possible all: 93.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1S7F

1s7f


Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 566 -random
Rwork0.193 ---
all0.193 10908 --
obs0.193 10908 96.5 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 53 64 1550
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_bond_d0.022
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.239

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