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- PDB-4f0y: Crystal structure of aminoglycoside antibiotic 6'-N-acetyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4f0y
TitleCrystal structure of aminoglycoside antibiotic 6'-N-acetyltransferase AAC(6')-IG from Acinetobacter haemolyticus, apo
ComponentsAminoglycoside N(6')-acetyltransferase type 1
KeywordsTRANSFERASE / Center for Structural Genomics of Infectious Diseases (CSGID) / NIAID / National Institute of Allergy and Infectious Diseases / GNAT superfamily / GCN5-related N-acetyltransferase superfamily / N-acetyltransferase fold / antibiotic resistance / aminoglycosides / acetyl Coenzyme A / intracellular
Function / homology
Function and homology information


aminoglycoside 6'-N-acetyltransferase / aminoglycoside 6'-N-acetyltransferase activity / response to antibiotic
Similarity search - Function
Aminoglycoside N6-acetyltransferase / 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
Aminoglycoside N(6')-acetyltransferase type 1
Similarity search - Component
Biological speciesAcinetobacter haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsStogios, P.J. / Evdokimova, E. / Dong, A. / Minasov, G. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: ACS Infect Dis. / Year: 2017
Title: Structural and Biochemical Characterization of Acinetobacter spp. Aminoglycoside Acetyltransferases Highlights Functional and Evolutionary Variation among Antibiotic Resistance Enzymes.
Authors: Stogios, P.J. / Kuhn, M.L. / Evdokimova, E. / Law, M. / Courvalin, P. / Savchenko, A.
History
DepositionMay 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Sep 13, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside N(6')-acetyltransferase type 1
B: Aminoglycoside N(6')-acetyltransferase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1389
Polymers37,7992
Non-polymers3397
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-62 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.963, 44.018, 46.576
Angle α, β, γ (deg.)83.19, 87.44, 72.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Aminoglycoside N(6')-acetyltransferase type 1 / AAC(6')-Ig / Aminoglycoside resistance protein


Mass: 18899.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter haemolyticus (bacteria) / Strain: BM2685 / Gene: AAC(6')-IG / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q44057, aminoglycoside 6'-N-acetyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Sep 7, 2011 / Details: VARIMAX HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.56→25 Å / Num. obs: 8914 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.039 / Net I/σ(I): 8.205
Reflection shellResolution: 2.56→2.61 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.095 / Num. unique all: 417 / Rsym value: 0.133 / % possible all: 94.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S3Z

1s3z


Resolution: 2.56→24.073 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 2.09 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 435 5.08 %RANDOM
Rwork0.1808 ---
obs0.1839 8893 85.28 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.678 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9215 Å2-4.556 Å2-0.2982 Å2
2--1.0122 Å24.1816 Å2
3----2.9337 Å2
Refinement stepCycle: LAST / Resolution: 2.56→24.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 17 84 2417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042388
X-RAY DIFFRACTIONf_angle_d0.6553238
X-RAY DIFFRACTIONf_dihedral_angle_d12.953864
X-RAY DIFFRACTIONf_chiral_restr0.046352
X-RAY DIFFRACTIONf_plane_restr0.002408
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.72030.37841300.25872367X-RAY DIFFRACTION81
2.7203-2.930.31841330.21512443X-RAY DIFFRACTION83
2.93-3.22420.2431250.20462409X-RAY DIFFRACTION84
3.2242-3.68930.22031340.17912508X-RAY DIFFRACTION86
3.6893-4.64270.20721360.1432544X-RAY DIFFRACTION87
4.6427-24.07430.21871390.16922607X-RAY DIFFRACTION90
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)
15.47140.6776-0.45285.7685-1.39615.89250.2042-0.0236-0.23550.2091-0.414-0.63710.03710.5020.13730.209-0.0098-0.04090.12560.03030.2434-6.52085.2684-0.5178
21.08660.4962-0.38071.9156-0.35741.33230.00370.0353-0.0496-0.2934-0.09010.17570.0571-0.00790.02620.14360.0296-0.0650.04770.01230.0488-15.381317.5834-3.565
33.2004-0.37170.72492.9408-0.8614.4667-0.0618-0.20960.22340.1816-0.07530.5651-0.0118-0.29010.12920.1527-0.00440.03460.2972-0.06590.2486-24.452338.22719.905
41.93610.3962-0.05341.6269-0.13292.46040.1152-0.26780.23110.1909-0.1505-0.0504-0.13550.07460.02380.1022-0.0696-0.01910.1022-0.04690.1163-10.845534.812714.6426
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:40
2X-RAY DIFFRACTION2chain A and resid 41:145
3X-RAY DIFFRACTION3chain B and resid 1:40
4X-RAY DIFFRACTION4chain B and resid 41:145

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