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- PDB-5isv: Crystal structure of the ribosomal-protein-S18-alanine N-acetyltr... -

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Basic information

Entry
Database: PDB / ID: 5isv
TitleCrystal structure of the ribosomal-protein-S18-alanine N-acetyltransferase from Escherichia coli
ComponentsRibosomal-protein-alanine acetyltransferase
KeywordsTRANSFERASE / RimI / AcCoA / GNAT / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


[ribosomal protein bS18]-alanine N-acetyltransferase / N-terminal peptidyl-alanine acetylation / peptide-alanine-alpha-N-acetyltransferase activity / N-terminal protein amino acid acetylation / protein modification process => GO:0036211 / internal peptidyl-lysine acetylation / N-acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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
[Ribosomal protein S18]-alanine N-acetyltransferase / [Ribosomal protein S18]-alanine N-acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFilippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Grimshaw, S. / Wolfe, A.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of the ribosomal-protein-S18-alanine N-acetyltransferase from Escherichia coli
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Grimshaw, S. / Wolfe, A.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosomal-protein-alanine acetyltransferase
B: Ribosomal-protein-alanine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)37,1832
Polymers37,1832
Non-polymers00
Water5,801322
1
A: Ribosomal-protein-alanine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)18,5921
Polymers18,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal-protein-alanine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)18,5921
Polymers18,5921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.222, 41.785, 46.404
Angle α, β, γ (deg.)93.74, 90.08, 116.52
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNASNASNAA2 - 1282 - 128
21ASNASNASNASNBB2 - 1282 - 128
12GLUGLUILEILEAA137 - 146137 - 146
22GLUGLUILEILEBB137 - 146137 - 146

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999901, -0.013934, -0.001825), (0.014051, -0.989203, -0.145879), (0.000227, -0.14589, 0.989301)67.22107, 105.12492, 31.04638

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Components

#1: Protein Ribosomal-protein-alanine acetyltransferase / Acetylating enzyme for N-terminal of ribosomal protein S18


Mass: 18591.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: rimI, Z5974, ECs5331 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic
References: UniProt: P0A946, UniProt: P0A944*PLUS, ribosomal-protein-alanine N-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 1.87 Å3/Da / Density % sol: 34.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.01 M tri-sodium citrate, 33% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 8, 2016 / Details: beryllium lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 56272 / % possible obs: 95 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 38.05
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.3 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CNT

2cnt


Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.731 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20902 2899 5.2 %RANDOM
Rwork0.15571 ---
obs0.15837 53373 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å21.85 Å2-1.03 Å2
2--0.02 Å2-0.36 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2463 0 0 323 2786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192658
X-RAY DIFFRACTIONr_bond_other_d0.0010.022469
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9423635
X-RAY DIFFRACTIONr_angle_other_deg1.17835661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52924.307137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12215435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7161520
X-RAY DIFFRACTIONr_chiral_restr0.1080.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023173
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02659
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9481.6751322
X-RAY DIFFRACTIONr_mcbond_other1.9461.6741321
X-RAY DIFFRACTIONr_mcangle_it2.4082.5231677
X-RAY DIFFRACTIONr_mcangle_other2.4072.5231678
X-RAY DIFFRACTIONr_scbond_it2.5822.0141336
X-RAY DIFFRACTIONr_scbond_other2.5842.0131337
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1032.9131959
X-RAY DIFFRACTIONr_long_range_B_refined4.55716.4793167
X-RAY DIFFRACTIONr_long_range_B_other3.95215.2223018
X-RAY DIFFRACTIONr_rigid_bond_restr2.18235127
X-RAY DIFFRACTIONr_sphericity_free36.4215101
X-RAY DIFFRACTIONr_sphericity_bonded12.81455294
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1950 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.425
Bloose thermal3.8410
LS refinement shellResolution: 1.349→1.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 170 -
Rwork0.22 3746 -
obs--89.35 %
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)
11.77220.21320.35230.8344-0.08912.5316-0.10950.1543-0.2086-0.1634-0.0249-0.01980.1425-0.02180.13440.0865-0.04540.04070.0596-0.02590.085922.178445.1608-11.1051
21.25420.29970.12490.68050.12281.4196-0.04370.10250.02570.01190.0526-0.01210.08380.0285-0.00890.054-0.04810.02520.0616-0.00830.074423.876347.4954-5.221
35.9561-0.83820.93330.79250.05640.2010.0135-0.0306-0.06980.14410.00340.00380.0511-0.016-0.0170.0748-0.04530.00920.05370.00480.040621.177146.17272.7286
42.0554-1.82571.49072.7053-1.35182.214-0.0004-0.15630.0340.04590.1419-0.0225-0.1045-0.1341-0.14160.0576-0.04790.02970.0708-0.00160.065823.558258.33451.5369
51.7396-0.71780.29863.4519-2.02933.0256-0.01410.08950.183-0.007-0.0285-0.1154-0.1840.0210.04250.0482-0.02870.02360.0327-0.00510.064324.789667.116-5.857
62.3627-1.26222.05520.9172-1.5952.8222-0.04620.00020.1135-0.0121-0.0181-0.06160.01090.05420.06430.0662-0.05150.03460.0525-0.02140.090635.477157.16776.7812
72.7029-0.0305-2.05013.39010.70172.15230.02750.15450.3345-0.2755-0.0027-0.0253-0.1410.1152-0.02480.0842-0.07410.01590.16240.0980.199147.598668.5497-32.4235
82.3288-1.3369-1.4721.94510.75613.6895-0.01860.19190.0045-0.1529-0.05550.0072-0.052-0.15070.07410.0634-0.04380.01060.05890.00740.061339.72362.1833-36.4514
93.55590.04260.24521.0904-0.22821.3705-0.02320.11750.17310.05490.0349-0.0066-0.05970.0278-0.01170.0362-0.02910.01820.0351-0.00290.051142.94964.0478-27.0008
103.86370.5652-0.46511.0493-0.03960.87460.0649-0.045-0.09450.2397-0.0291-0.0412-0.11610.0866-0.03580.1086-0.05920.00760.0630.00270.046843.072761.7342-19.5664
112.7786-1.48850.40121.85860.63734.92590.0801-0.0008-0.2442-0.09550.00070.17150.37350.1428-0.08070.0747-0.0111-0.00530.0288-0.0020.052843.39646.9214-25.6501
123.1381-1.0283-2.78260.42941.09753.3558-0.0117-0.009-0.1724-0.0026-0.00060.04450.02620.01910.01230.0545-0.02890.01470.0243-0.00080.075633.795750.5349-19.7625
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 46
2X-RAY DIFFRACTION2A47 - 73
3X-RAY DIFFRACTION3A74 - 96
4X-RAY DIFFRACTION4A97 - 119
5X-RAY DIFFRACTION5A120 - 135
6X-RAY DIFFRACTION6A136 - 155
7X-RAY DIFFRACTION7B2 - 22
8X-RAY DIFFRACTION8B23 - 41
9X-RAY DIFFRACTION9B42 - 73
10X-RAY DIFFRACTION10B74 - 101
11X-RAY DIFFRACTION11B102 - 131
12X-RAY DIFFRACTION12B132 - 155

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