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- PDB-5e96: Crystal structure of aminoglycoside 6'-acetyltransferase type Ii -

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Basic information

Entry
Database: PDB / ID: 5.0E+96
TitleCrystal structure of aminoglycoside 6'-acetyltransferase type Ii
ComponentsAminoglycoside 6'-acetyltransferase
KeywordsTRANSFERASE / GNAT / acetyltransferase / aminoglycoside resistance
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
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
PHOSPHATE ION / : / Aac(6')-Ii protein
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBerghuis, A.M. / Burk, D.L. / Baettig, O.M. / Shi, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-13107 Canada
CitationJournal: Febs J. / Year: 2016
Title: Comprehensive characterization of ligand-induced plasticity changes in a dimeric enzyme.
Authors: Baettig, O.M. / Shi, K. / Yachnin, B.J. / Burk, D.L. / Berghuis, A.M.
History
DepositionOct 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminoglycoside 6'-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6723
Polymers20,5151
Non-polymers1572
Water95553
1
A: Aminoglycoside 6'-acetyltransferase
hetero molecules

A: Aminoglycoside 6'-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3446
Polymers41,0302
Non-polymers3144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area2780 Å2
ΔGint-25 kcal/mol
Surface area15930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.815, 66.815, 104.129
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Aminoglycoside 6'-acetyltransferase


Mass: 20514.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Strain: C238 / Gene: aac(6 )-II / Plasmid: pPLaac-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A099R279, UniProt: Q47764*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.27 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% ethylene glycol, 0.1 M phosphate-citrate pH 4.2, 0.1 M ammonium sulfate
PH range: 4.2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15426 / % possible obs: 99.9 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 22.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.206 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
PDB_EXTRACT3.15data extraction
PHASER1.3.1phasing
SCALEPACKdata scaling
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N71

1n71


Resolution: 2.1→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1497 9.7 %RANDOM SELECTION
Rwork0.217 ---
obs0.217 14868 96.5 %-
Solvent computationBsol: 53.98 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1-4.501 Å20 Å20 Å2
2--4.501 Å20 Å2
3----9.002 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-50 Å
Luzzati sigma a-0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 9 53 1307
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5891.5
X-RAY DIFFRACTIONc_mcangle_it2.6672
X-RAY DIFFRACTIONc_scbond_it1.9552
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2.1→2.12 Å / Total num. of bins used: 29 /
RfactorNum. reflection
Rfree0.3066 53
Rwork0.2905 424
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAMCNS_TOPPAR:PROTEIN.TOP
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAMCNS_TOPPAR:DNA-RNA.TOP
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAMCNS_TOPPAR:WATER.TOP
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAMCNS_TOPPAR:ION.TOP
X-RAY DIFFRACTION5EDO.PAREDO.TOP

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