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- PDB-2prb: crystal structure of aminoglycoside acetyltransferase AAC(6')-Ib ... -

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Basic information

Entry
Database: PDB / ID: 2prb
Titlecrystal structure of aminoglycoside acetyltransferase AAC(6')-Ib in complex whith coenzyme A
ComponentsAminoglycoside 6-N-acetyltransferase type Ib11
KeywordsTRANSFERASE / GNAT / aminoglycoside 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
COENZYME A / Aminoglycoside N(6')-acetyltransferase type 1
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Aug 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)22,6892
Polymers21,9211
Non-polymers7681
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.620, 57.620, 146.672
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) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5 M K2HPO4 0.06M NaH2PO4 0.1M guanidine-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 3, 2007
RadiationMonochromator: diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.8→53.63 Å / Num. all: 23842 / Num. obs: 23836 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 13.5 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 8.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 4.1 / Num. measured all: 35626 / Num. unique all: 3394 / Rsym value: 0.183 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å40.74 Å
Translation2.5 Å40.74 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 2PR8

2pr8


Resolution: 1.8→40.76 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.2 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1219 5.1 %RANDOM
Rwork0.209 ---
all0.209 23765 --
obs0.21 23761 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: 15.468 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 48 172 1580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221440
X-RAY DIFFRACTIONr_angle_refined_deg1.00321968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8595171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8422465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.48515226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2291511
X-RAY DIFFRACTIONr_chiral_restr0.0630.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021083
X-RAY DIFFRACTIONr_nbd_refined0.1760.2653
X-RAY DIFFRACTIONr_nbtor_refined0.2950.2989
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0870.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.218
X-RAY DIFFRACTIONr_mcbond_it0.4111.5889
X-RAY DIFFRACTIONr_mcangle_it0.75321384
X-RAY DIFFRACTIONr_scbond_it1.0443644
X-RAY DIFFRACTIONr_scangle_it1.8044.5584
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 93 -
Rwork0.238 1611 -
obs-1704 100 %

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