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- PDB-2cnt: RimI - Ribosomal S18 N-alpha-protein acetyltransferase in complex... -

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Basic information

Entry
Database: PDB / ID: 2cnt
TitleRimI - Ribosomal S18 N-alpha-protein acetyltransferase in complex with CoenzymeA.
ComponentsMODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
KeywordsTRANSFERASE / N-ALPHA ACETYLATION / GCN5-N-ACETYLTRANSFERASE / RIBOSOMAL PROTEIN / ACETYLTRANSFERASE / GNAT / ACYLTRANSFERASE
Function / homology
Function and homology information


[ribosomal protein bS18]-alanine N-acetyltransferase / protein-N-terminal-alanine acetyltransferase activity / cytoplasm
Similarity search - Function
N-acetyltransferase RimI / N-acetyltransferase RimI/Ard1 / : / Acetyltransferase (GNAT) family / 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 / [Ribosomal protein bS18]-alanine N-acetyltransferase
Similarity search - Component
Biological speciesSALMONELLA TYPHIMURIUM (bacteria)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.4 Å
AuthorsVetting, M.W. / Bareich, D.C. / Yu, M. / Blanchard, J.S.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal Structure of Rimi from Salmonella Typhimurium Lt2, the Gnat Responsible for N{Alpha}- Acetylation of Ribosomal Protein S18.
Authors: Vetting, M.W. / Bareich, D.C. / Yu, M. / Blanchard, J.S.
History
DepositionMay 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
B: MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
C: MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
D: MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,83813
Polymers73,3034
Non-polymers3,5359
Water4,179232
1
A: MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1853
Polymers18,3261
Non-polymers8602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2814
Polymers18,3261
Non-polymers9563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1853
Polymers18,3261
Non-polymers8602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1853
Polymers18,3261
Non-polymers8602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.926, 126.926, 113.859
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein
MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18 / RIBOSOMAL-N-ALPHA-ACETYLTRANSFERASE


Mass: 18325.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA TYPHIMURIUM (bacteria) / Strain: LT2 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q8ZJW4, ribosomal-protein-alanine N-acetyltransferase
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE PROTEIN IS A MONOMER IN SOLUTION. THE OBSERVED TRIMERS IN THE UNIT CELL ARE NON-PHYSIOLOGICAL.

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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: 3.78 Å3/Da / Density % sol: 67.6 %
Crystal growpH: 5 / Details: 2.2-2.8 M (NH4)2SO4, 100 MM MES PH 4.5-5.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: MARRESEARCH RAXIS IV / Detector: IMAGE PLATE / Details: OSMIC CONFOCAL MAXFLUX OPTICS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 39657 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4data scaling
SOLVERESOLVE ARP WARP AMORE CCP4phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→113.96 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.276 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2108 5 %RANDOM
Rwork0.186 ---
obs0.188 39657 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.4→113.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 221 232 5261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225131
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9936993
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8723.667240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87915820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8831540
X-RAY DIFFRACTIONr_chiral_restr0.0980.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023816
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.22187
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23423
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.691.53105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.21924831
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.07932336
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3744.52162
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 155
Rwork0.244 2858
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)
14.354-1.1838-0.01521.47060.24890.8247-0.151-0.5994-0.21020.18240.16920.06530.0976-0.038-0.0182-0.10540.00770.04790.11370.088-0.2366-5.99545.32949.477
22.86160.21580.7281.77280.1161.9762-0.1402-0.1360.0890.03320.01710.1248-0.127-0.21020.1231-0.15670.04010.0134-0.1224-0.0498-0.216342.0138.1559.324
31.95260.2080.25561.91660.59592.7591-0.07180.013-0.09290.03970.1211-0.1556-0.03130.1083-0.0493-0.16960.05290.0152-0.1141-0.0124-0.238128.60851.638.151
42.27230.0732-0.40281.7675-0.61143.65410.02560.0901-0.2734-0.16280.08680.07240.3821-0.3227-0.1124-0.1031-0.06470.0049-0.0620.0111-0.15753.94835.44115.072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 151
2X-RAY DIFFRACTION2B1 - 151
3X-RAY DIFFRACTION3C1 - 151
4X-RAY DIFFRACTION4D1 - 151

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