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- PDB-1n71: Crystal structure of aminoglycoside 6'-acetyltransferase type Ii ... -

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Basic information

Entry
Database: PDB / ID: 1n71
TitleCrystal structure of aminoglycoside 6'-acetyltransferase type Ii in complex with coenzyme A
Componentsaac(6')-Ii
KeywordsTRANSFERASE / AMINOGLYCOSIDE 6'-N-ACETYLTRANSFERASE / ANTIBIOTIC RESISTANCE / COENZYME A
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
COENZYME A / Aac(6')-Ii protein
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBurk, D.L. / Ghuman, N. / Wybenga-Groot, L.E. / Berghuis, A.M.
Citation
Journal: Protein Sci. / Year: 2003
Title: X-ray structure of the AAC(6')-Ii antibiotic resistance enzyme at 1.8 A resolution; examination of oligomeric arrangements in GNAT superfamily members
Authors: Burk, D.L. / Ghuman, N. / Wybenga-Groot, L.E. / Berghuis, A.M.
#1: Journal: Structure / Year: 1999
Title: Crystal structure of an aminoglycoside 6'-N-acetyltransferase: defining the GCN5-related N-acetyltransferase superfamily fold
Authors: Wybenga-Groot, L.E. / Draker, K. / Wright, G.D. / Berghuis, A.M.
History
DepositionNov 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The author states that there is an error in the sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aac(6')-Ii
B: aac(6')-Ii
C: aac(6')-Ii
D: aac(6')-Ii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,61013
Polymers82,0604
Non-polymers3,5509
Water9,080504
1
A: aac(6')-Ii
B: aac(6')-Ii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5654
Polymers41,0302
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-12 kcal/mol
Surface area16730 Å2
MethodPISA
2
C: aac(6')-Ii
D: aac(6')-Ii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0459
Polymers41,0302
Non-polymers2,0157
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-65 kcal/mol
Surface area16860 Å2
MethodPISA
3
C: aac(6')-Ii
D: aac(6')-Ii
hetero molecules

A: aac(6')-Ii
B: aac(6')-Ii
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,61013
Polymers82,0604
Non-polymers3,5509
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area14300 Å2
ΔGint-93 kcal/mol
Surface area30850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.190, 76.920, 130.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAsymmetric unit contains two biological units (dimers)

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Components

#1: Protein
aac(6')-Ii


Mass: 20514.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Plasmid: pPLaac-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q47764
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.02 Å3/Da / Density % sol: 38.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
21 Mammonium sulfate1drop
32 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0722 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 1.8→27.97 Å / Num. all: 64971 / Num. obs: 64971 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.1
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 100 Å / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 67.6 % / Redundancy: 3.1 % / Num. unique obs: 4590 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1B87 with cofactor and water removed

1b87


Resolution: 1.8→27.97 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 6300 10.1 %RANDOM
Rwork0.208 ---
all0.208 ---
obs0.208 62541 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5792 Å2 / ksol: 0.359296 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.1 Å20 Å20 Å2
2---4.98 Å20 Å2
3----0.12 Å2
Refine analyzeLuzzati coordinate error free: 0.26 Å / Luzzati sigma a free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5766 0 217 504 6487
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 746 10.3 %
Rwork0.265 6515 -
obs--64.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2COA.PARCOA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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