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- PDB-2qir: Crystal structure of aminoglycoside acetyltransferase AAC(6')-Ib ... -

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Basic information

Entry
Database: PDB / ID: 2qir
TitleCrystal structure of aminoglycoside acetyltransferase AAC(6')-Ib in complex whith coenzyme A and kanamycin
ComponentsAminoglycoside 6-N-acetyltransferase type Ib11
KeywordsTRANSFERASE / Aminoglycoside resistance / acetyltransferase
Function / homology
Function and homology information


aminoglycoside 6'-N-acetyltransferase / N-acyltransferase activity / response to antibiotic
Similarity search - Function
Aminoglycoside N(6')-acetyltransferase, AacA4 type / Acetyltransferase (GNAT) domain / 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
Chem-9CS / COENZYME A / Aminoglycoside N(6')-acetyltransferase type 1
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMaurice, F. / Broutin, I. / Podglajen, I. / Benas, P. / Collatz, E. / Dardel, F.
CitationJournal: Embo Rep. / Year: 2008
Title: Enzyme structural plasticity and the emergence of broad-spectrum antibiotic resistance.
Authors: Maurice, F. / Broutin, I. / Podglajen, I. / Benas, P. / Collatz, E. / Dardel, F.
History
DepositionJul 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 7, 2016Group: Non-polymer description
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoglycoside 6-N-acetyltransferase type Ib11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1723
Polymers21,9211
Non-polymers1,2512
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.404, 57.404, 145.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Aminoglycoside 6-N-acetyltransferase type Ib11


Mass: 21921.439 Da / Num. of mol.: 1 / Mutation: L106Q, S107L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: aac(6')-Ib / Plasmid: pET101 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8GLI5, aminoglycoside 6'-N-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-9CS / (1R,2S,3S,4R,6S)-4,6-DIAMINO-3-[(3-AMINO-3-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]-2-HYDROXYCYCLOHEXYL 2,6-DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSIDE / Kanamycin B / Bekanamycin


Mass: 483.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37N5O10
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: K2HPO4 1.5 M, NaH2PO4 0.06M, Guanidine 0.1M, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→53.402 Å / Num. all: 10187 / Num. obs: 10187 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 13.4 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.5311.50.2123.41640714270.212100
2.53-2.6814.30.184.11945513620.18100
2.68-2.8714.20.1325.51844713010.132100
2.87-3.114.10.1027.31691811980.102100
3.1-3.39140.0779.11589611370.077100
3.39-3.813.90.06111.11414810160.061100
3.8-4.3813.70.05113124639100.051100
4.38-5.3713.30.05211.9105967960.052100
5.37-7.5912.70.069.780576360.06100
7.59-72.7910.60.05610.842704040.05699.8

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å53.4 Å
Translation2.5 Å53.4 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2prb

2prb


Resolution: 2.4→45.08 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.892 / SU B: 5.865 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R: 0.305 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 490 4.8 %RANDOM
Rwork0.192 ---
all0.192 10187 --
obs0.194 10125 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.601 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1356 0 81 78 1515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221471
X-RAY DIFFRACTIONr_angle_refined_deg1.3492.0372015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4115170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2542465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08615226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6721511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021079
X-RAY DIFFRACTIONr_nbd_refined0.1960.2629
X-RAY DIFFRACTIONr_nbtor_refined0.30.21001
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3850.218
X-RAY DIFFRACTIONr_mcbond_it0.751.5884
X-RAY DIFFRACTIONr_mcangle_it1.20221379
X-RAY DIFFRACTIONr_scbond_it1.7043679
X-RAY DIFFRACTIONr_scangle_it2.8424.5636
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 37 -
Rwork0.203 681 -
obs-718 100 %

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