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- PDB-4e8o: Crystal structure of aminoglycoside antibiotic 6'-N-acetyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4e8o
TitleCrystal structure of aminoglycoside antibiotic 6'-N-acetyltransferase AAC(6')-Ih from Acinetobacter baumannii
ComponentsAac(6')-Ih protein
KeywordsTRANSFERASE / antibiotic resistance / 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 / aminoglycoside antibiotic 6'-N-acetyltransferase / aminoglycoside antibiotics / acetyl coenzyme A / coenzyme A / intracellular
Function / homology
Function and homology information


aminoglycoside 6'-N-acetyltransferase activity / aminoglycoside 6'-N-acetyltransferase / 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 baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.138 Å
AuthorsStogios, P.J. / Minasov, G. / Dong, A. / Evdokimova, E. / 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
DepositionMar 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references / Structure summary
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Feb 22, 2017Group: Database references
Revision 1.4Sep 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 / 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 / _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

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Assembly

Deposited unit
A: Aac(6')-Ih protein
B: Aac(6')-Ih protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5619
Polymers38,3132
Non-polymers2487
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-84 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.963, 46.048, 46.082
Angle α, β, γ (deg.)102.55, 97.13, 111.21
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Aac(6')-Ih protein


Mass: 19156.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: BM2686 / Gene: aac(6')-Ih / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q43899, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 1.96 Å3/Da / Density % sol: 37.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG5000 MME, 0.1 M Bis-Tris, pH 6.5, 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 SATURN A200 / Detector: CCD / Date: Sep 7, 2011 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.138→25 Å / Num. all: 16092 / Num. obs: 15384 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 0.033 / Net I/σ(I): 11.65
Reflection shellResolution: 2.138→2.18 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.05 / Rsym value: 0.151 / % possible all: 92

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Processing

Software
NameVersionClassification
StructureStudiodata 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: 2.138→23.497 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 2.09 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2276 770 5.01 %random
Rwork0.1861 ---
obs0.1883 15377 95.38 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.363 Å2 / ksol: 0.398 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2672 Å23.2359 Å2-0.9984 Å2
2--0.0987 Å22.5874 Å2
3----3.366 Å2
Refinement stepCycle: LAST / Resolution: 2.138→23.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 7 137 2512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042439
X-RAY DIFFRACTIONf_angle_d0.8053313
X-RAY DIFFRACTIONf_dihedral_angle_d14.564884
X-RAY DIFFRACTIONf_chiral_restr0.056367
X-RAY DIFFRACTIONf_plane_restr0.003430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.138-2.30310.24731500.21212843X-RAY DIFFRACTION92
2.3031-2.53470.24941520.21312885X-RAY DIFFRACTION95
2.5347-2.90090.24681530.20862919X-RAY DIFFRACTION95
2.9009-3.65260.22851550.17752945X-RAY DIFFRACTION97
3.6526-23.49810.20951600.17193015X-RAY DIFFRACTION98
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)
16.5517-0.82531.41044.45432.03894.4098-0.0191-0.24-0.08150.22390.1327-0.3912-0.13880.6272-0.07850.2517-0.0536-0.00930.37350.01320.1549.03-45.927-4.3479
21.74190.01320.87372.4416-0.73453.76520.1094-0.2024-0.23470.0490.18570.0160.4765-0.3631-0.24870.2202-0.0244-0.0190.21190.01360.1854-1.235-46.908-17.986
33.5377-0.2530.22182.08010.73252.285-0.23040.18380.2861-0.3214-0.00330.4463-0.2734-0.4440.10460.23490.0016-0.06710.2325-0.00040.3034-17.0634-22.5367-33.4472
43.2103-1.17840.89063.3562-0.6282.5573-0.07780.18970.3422-0.06180.0286-0.278-0.06010.03640.04310.1548-0.04010.02260.197-0.00910.1855-1.319-29.0139-30.4175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 0:58
2X-RAY DIFFRACTION2chain A and resid 59:146
3X-RAY DIFFRACTION3chain B and resid -1:58
4X-RAY DIFFRACTION4chain B and resid 59:146

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