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- PDB-6bfh: Structure of the kanamycin complex of aminoglycoside acetyltransf... -

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Basic information

Entry
Database: PDB / ID: 6bfh
TitleStructure of the kanamycin complex of aminoglycoside acetyltransferase AAC(6')-Im
ComponentsAminoglycoside acetyltransferase
KeywordsTRANSFERASE / antibiotic resistance / aminoglycoside / acetyltransferase
Function / homology
Function and homology information


acetyltransferase activity
Similarity search - Function
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
KANAMYCIN A / Aminoglycoside acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1803
Polymers21,6041
Non-polymers5772
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.750, 107.750, 37.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Aminoglycoside acetyltransferase


Mass: 21603.604 Da / Num. of mol.: 1
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-KAN / KANAMYCIN A / Kanamycin A


Mass: 484.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→34.7 Å / Num. obs: 18370 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 18.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1332 / CC1/2: 0.894 / % possible all: 98.4

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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: 1.95→25.881 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 942 5.14 %
Rwork0.1705 17395 -
obs0.1717 18337 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.61 Å2 / Biso mean: 38.6375 Å2 / Biso min: 20.08 Å2
Refinement stepCycle: final / Resolution: 1.95→25.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 39 98 1639
Biso mean--42.09 41.39 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081583
X-RAY DIFFRACTIONf_angle_d0.9162140
X-RAY DIFFRACTIONf_chiral_restr0.061228
X-RAY DIFFRACTIONf_plane_restr0.005271
X-RAY DIFFRACTIONf_dihedral_angle_d17.932959
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9501-2.05280.26771460.21524572603
2.0528-2.18140.21541390.189824492588
2.1814-2.34970.22521350.174724552590
2.3497-2.5860.21811330.178324832616
2.586-2.95970.20831400.180224572597
2.9597-3.72710.18631310.176125242655
3.7271-25.8830.16461180.151925702688
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)
12.07030.51210.84522.7891-0.21172.8572-0.04770.1697-0.0282-0.47880.0654-0.2993-0.24590.258400.4211-0.1230.02080.3174-0.02510.363438.0862-23.4672-7.3792
21.10431.82880.34033.4747-1.24713.6009-0.09570.00790.15520.17370.1698-0.076-0.2923-0.0105-0.00010.3582-0.0889-0.00760.2702-0.04550.372133.4495-21.90550.8354
31.42490.72180.27383.642-0.55892.9004-0.0174-0.0870.057-0.28530.0768-0.00570.06740.04420.00020.2975-0.0274-0.00730.2432-0.01660.258331.0833-34.27810.3595
42.7915-0.1162-0.14692.06860.87050.8852-0.1390.29250.1109-0.1609-0.0172-0.0629-0.10380.195-0.00050.3435-0.0503-0.03190.2220.00990.250528.8042-39.0788-7.9315
51.78060.8042-0.67291.40180.91671.73590.03980.21070.1527-0.4778-0.03270.4671-0.0949-0.224-0.00070.4286-0.0179-0.06810.252-0.00370.302122.3709-37.099-8.3396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 41 )A3 - 41
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 66 )A42 - 66
3X-RAY DIFFRACTION3chain 'A' and (resid 67 through 127 )A67 - 127
4X-RAY DIFFRACTION4chain 'A' and (resid 128 through 149 )A128 - 149
5X-RAY DIFFRACTION5chain 'A' and (resid 150 through 178 )A150 - 178

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