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- PDB-6bff: Structure of the aminoglycoside acetyltransferase AAC(6')-Im -

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Basic information

Entry
Database: PDB / ID: 6bff
TitleStructure of the aminoglycoside acetyltransferase AAC(6')-Im
ComponentsAminoglycoside acetyltransferase
KeywordsTRANSFERASE / antibiotic resistance / aminoglycoside / acetyltransferase
Function / homologyGcn5-related N-acetyltransferase (GNAT) / acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / Aminoglycoside acetyltransferase
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI057393 United States
CitationJournal: Microb Cell / Year: 2017
Title: Aminoglycoside resistance profile and structural architecture of the aminoglycoside acetyltransferase AAC(6')-Im.
Authors: Smith, C.A. / Bhattacharya, M. / Toth, M. / Stewart, N.K. / Vakulenko, S.B.
History
DepositionOct 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside acetyltransferase
B: Aminoglycoside acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2564
Polymers43,2072
Non-polymers492
Water4,918273
1
A: Aminoglycoside acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6282
Polymers21,6041
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoglycoside acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6282
Polymers21,6041
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.550, 34.950, 67.320
Angle α, β, γ (deg.)90.000, 102.330, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

21B-432-

HOH

31B-434-

HOH

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Components

#1: Protein Aminoglycoside acetyltransferase


Mass: 21603.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aac(6')-Im / Production host: Escherichia coli (E. coli) / References: UniProt: Q93ET8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, 0.1 M Tris HCl pH 8.5, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→39.6 Å / Num. obs: 39826 / % possible obs: 96.9 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.9
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2771 / CC1/2: 0.784 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QC6

4qc6


Resolution: 1.7→34.123 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.43
RfactorNum. reflection% reflection
Rfree0.2293 2012 5.05 %
Rwork0.1846 --
obs0.1868 39826 97.07 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 87.83 Å2 / Biso mean: 28.0345 Å2 / Biso min: 9.14 Å2
Refinement stepCycle: final / Resolution: 1.7→34.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 2 275 3311
Biso mean--25.9 33.73 -
Num. residues----356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083123
X-RAY DIFFRACTIONf_angle_d0.9314195
X-RAY DIFFRACTIONf_chiral_restr0.062429
X-RAY DIFFRACTIONf_plane_restr0.006542
X-RAY DIFFRACTIONf_dihedral_angle_d15.471881
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.42811370.34532589272694
1.7425-1.78970.32851240.3182657278196
1.7897-1.84230.34181460.2612627277395
1.8423-1.90180.26821620.23042662282497
1.9018-1.96970.22951520.19082675282798
1.9697-2.04860.22921490.18352743289298
2.0486-2.14180.22531330.17582664279798
2.1418-2.25470.22181390.17982693283297
2.2547-2.3960.28051380.18562739287799
2.396-2.58090.23171540.18992728288298
2.5809-2.84050.21331450.18722678282395
2.8405-3.25120.23761330.18512764289799
3.2512-4.09510.18991530.15742723287697
4.0951-34.13010.2091470.16732872301998
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)
12.65430.02350.24453.03280.23462.1065-0.0184-0.10990.04270.173-0.03170.055-0.0663-0.09890.04920.10310.0177-0.01890.1231-0.00830.09666.3377-0.45385.6102
24.87091.50830.13540.93690.08530.02890.1856-0.67810.35260.4528-0.25610.1304-0.587-0.38550.07120.44320.06670.01460.5114-0.05190.31616.5158.02817.6623
32.8272-0.16041.36291.13730.25431.9585-0.0775-0.01970.11280.0453-0.0286-0.0911-0.10460.07480.10450.1604-0.00450.02150.13850.01660.134819.31351.91428.8076
42.5168-0.6141-0.69781.7414-0.39663.1389-0.0172-0.1331-0.28060.0556-0.0126-0.05060.2022-0.050.05270.14-0.0102-0.0080.17210.02450.169522.2549-8.728413.9534
51.8699-0.08360.30761.89980.21991.650.13890.1628-0.1496-0.1466-0.2004-0.01040.06430.1390.04820.17320.04940.00110.17860.01190.16164.87341.224524.5324
64.38931.76183.51750.76941.5162.98770.5283-0.7844-0.71960.2042-0.20290.36330.8919-0.5154-0.44380.4065-0.0141-0.00150.33680.16620.524257.9484-8.020432.7661
73.3077-0.07780.47162.1102-0.3531.76530.10370.1525-0.38-0.1455-0.12650.14640.118-0.0230.01670.15990.0188-0.00880.1003-0.02310.149852.5343-1.078518.8131
82.544-0.53230.38152.1054-0.02333.0624-0.0186-0.04030.2524-0.0165-0.08910.0921-0.1766-0.0950.10680.14660.0053-0.00520.1779-0.00520.185247.09389.257822.3426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 41 )A1 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 56 )A42 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 140 )A57 - 140
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 178 )A141 - 178
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 41 )B2 - 41
6X-RAY DIFFRACTION6chain 'B' and (resid 42 through 56 )B42 - 56
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 140 )B57 - 140
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 178 )B141 - 178

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