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

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Basic information

Entry
Database: PDB / ID: 4evy
TitleCrystal structure of aminoglycoside antibiotic 6'-N-acetyltransferase AAC(6')-Ig from Acinetobacter haemolyticus in complex with tobramycin
ComponentsAminoglycoside N(6')-acetyltransferase type 1
KeywordsTRANSFERASE/ANTIBIOTIC / 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 / acetyl coenzyme A / intracellular / TRANSFERASE-ANTIBIOTIC complex
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
: / TOBRAMYCIN / Aminoglycoside N(6')-acetyltransferase type 1
Similarity search - Component
Biological speciesAcinetobacter haemolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.768 Å
AuthorsStogios, P.J. / Evdokimova, E. / 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
DepositionApr 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 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_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.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)38,9189
Polymers37,7992
Non-polymers1,1207
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-61 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.723, 43.789, 46.282
Angle α, β, γ (deg.)83.65, 87.49, 68.41
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-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL


Mass: 467.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37N5O9 / Comment: antibiotic*YM
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.05 M magnesium chloride, 25% PEG3350, 0.05 M trisodium citrate dihydrate, pH 4.6, 5 mM tobramicin, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 5, 2012
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.768→30 Å / Num. all: 28099 / Num. obs: 26273 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.051 / Net I/σ(I): 40.79
Reflection shellResolution: 1.768→1.8 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.91 / Rsym value: 0.658 / % possible all: 87.3

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Processing

Software
NameVersionClassification
CrystalCleardata 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: 1.768→28.971 Å / SU ML: 0.28 / σ(F): 1.96 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2134 1245 5 %
Rwork0.1669 --
obs0.1692 25205 91.87 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.352 Å2 / ksol: 0.375 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.0773 Å2-3.2265 Å2-1.4358 Å2
2---1.5335 Å22.0132 Å2
3----2.5438 Å2
Refinement stepCycle: LAST / Resolution: 1.768→28.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 69 223 2621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122503
X-RAY DIFFRACTIONf_angle_d1.3563396
X-RAY DIFFRACTIONf_dihedral_angle_d15.41939
X-RAY DIFFRACTIONf_chiral_restr0.099391
X-RAY DIFFRACTIONf_plane_restr0.006422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.768-1.8020.35941290.34692478X-RAY DIFFRACTION82
1.802-1.83870.34581380.32342620X-RAY DIFFRACTION90
1.8387-1.87870.30671480.29642757X-RAY DIFFRACTION91
1.8787-1.92240.31231400.25012667X-RAY DIFFRACTION91
1.9224-1.97050.30221440.22452745X-RAY DIFFRACTION92
1.9705-2.02370.28491410.19152678X-RAY DIFFRACTION91
2.0237-2.08330.23651470.17992811X-RAY DIFFRACTION92
2.0833-2.15050.25991440.16292725X-RAY DIFFRACTION92
2.1505-2.22730.18161420.17372772X-RAY DIFFRACTION93
2.2273-2.31650.2831460.16582747X-RAY DIFFRACTION93
2.3165-2.42180.2411460.18172785X-RAY DIFFRACTION94
2.4218-2.54940.23741470.17112783X-RAY DIFFRACTION94
2.5494-2.70910.2521480.18932790X-RAY DIFFRACTION94
2.7091-2.91810.27181460.18142785X-RAY DIFFRACTION93
2.9181-3.21140.23961410.16572715X-RAY DIFFRACTION93
3.2114-3.67530.17541470.1462739X-RAY DIFFRACTION91
3.6753-4.62740.13571490.12332825X-RAY DIFFRACTION94
4.6274-28.97520.17631450.14392799X-RAY DIFFRACTION94
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)
17.61010.5001-0.13845.6677-1.30755.76710.10690.2171-0.2134-0.0803-0.3871-0.36540.53830.86960.20520.21950.034-0.0510.14930.04410.1743-6.34125.6520.6989
21.59440.27120.16813.65640.17942.9862-0.00970.1628-0.0617-0.26920.00730.18780.1632-0.0326-0.00190.1076-0-0.02580.1230.00350.1003-14.11918.5922-2.3978
35.9245-2.00321.25712.2622-0.7138.5795-0.2062-0.58160.11210.42460.25780.3498-0.649-0.5884-0.01280.2630.02620.05360.2246-0.010.221-23.180937.74620.6829
41.96420.5599-0.2522.4359-0.06663.30020.0474-0.18750.17650.2135-0.0382-0.0239-0.32440.19680.00880.1875-0.018-0.00810.1375-0.00780.1345-9.260734.856514.8491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 1:40
2X-RAY DIFFRACTION2chain A and resi 41:145
3X-RAY DIFFRACTION3chain B and resi 1:40
4X-RAY DIFFRACTION4chain B and resi 41:145

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