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- PDB-2pr8: crystal structure of aminoglycoside N-acetyltransferase AAC(6')-Ib11 -

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Basic information

Entry
Database: PDB / ID: 2pr8
Titlecrystal structure of aminoglycoside N-acetyltransferase AAC(6')-Ib11
ComponentsAminoglycoside 6-N-acetyltransferase type Ib11
KeywordsTRANSFERASE / GNAT / aminoglycoside acetyltransferase
Function / homology
Function and homology information


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
Aminoglycoside 6-N-acetyltransferase type Ib11
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,2374
Polymers43,7612
Non-polymers4772
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.620, 85.370, 150.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe second part of the biological assembly is generated by a two fold axis

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Components

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


Mass: 21880.389 Da / Num. of mol.: 2
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0,1 M Hepes pH7.5 1.5 M lithium sulfate 3 % isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1771
2771
3771
4771
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF BM30A20.9794
SYNCHROTRONESRF BM30A30.9792
SYNCHROTRONESRF BM30A40.931
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDSep 26, 2005
ADSC QUANTUM 3152CCDFeb 27, 2006
ADSC QUANTUM 3153CCDFeb 27, 2006
ADSC QUANTUM 3154CCDFeb 27, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamond (111)SINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
3Si 111MADMx-ray1
4Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.97941
30.97921
40.9311
Reflection
IDAv σ(I) over netINumberRmerge(I) obsD res high (Å)Num. obs% possible obs
125.09432600.0242.82221197.1
229.19899180.0322.792271798.9
319.75440250.032.82248498.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obs
5.8237.197.610.023
4.795.8298.710.026
4.174.7997.410.021
3.744.1799.210.021
3.423.7499.710.022
3.173.4299.910.024
2.973.1710010.028
2.82.979210.033
5.8837.199.720.032
4.815.8899.820.035
4.184.8199.820.029
3.744.1810020.03
3.413.7410020.029
3.163.4110020.032
2.963.1610020.037
2.792.9695.420.041
5.737.199.530.027
4.745.799.930.026
4.144.7499.930.025
3.724.1410030.026
3.413.7210030.029
3.163.4110030.034
2.973.1699.930.045
2.82.9793.430.052
ReflectionResolution: 2.1→37.1 Å / Num. all: 26857 / Num. obs: 26857 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 28.49 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 20.42
Reflection shellResolution: 2.1→2.23 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 7.3 / Num. measured obs: 15578 / Num. unique all: 4253 / % possible all: 97.3

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Phasing

PhasingMethod: MAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.837.6200105151453
ISO_22.837.621.4150.899104161387
ISO_32.837.622.3031.309104901407
ANO_12.837.625.070105080
ANO_22.837.623.2650103650
ANO_32.837.621.6640105000
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_111.91-37.62009660
ISO_18.64-11.910019263
ISO_17.12-8.640025970
ISO_16.19-7.120031968
ISO_15.55-6.190036778
ISO_15.08-5.550040476
ISO_14.71-5.080044570
ISO_14.41-4.710049275
ISO_14.16-4.410051676
ISO_13.95-4.160054271
ISO_13.77-3.950055674
ISO_13.61-3.770061970
ISO_13.47-3.610063381
ISO_13.34-3.470065167
ISO_13.23-3.340068080
ISO_13.13-3.230068674
ISO_13.04-3.130076375
ISO_12.95-3.040073178
ISO_12.87-2.950078971
ISO_12.8-2.870077576
ANO_111.91-37.622.0580960
ANO_18.64-11.916.74701890
ANO_17.12-8.647.92202590
ANO_16.19-7.128.26903190
ANO_15.55-6.197.87103670
ANO_15.08-5.556.63204040
ANO_14.71-5.085.37204440
ANO_14.41-4.715.38504900
ANO_14.16-4.414.705160
ANO_13.95-4.165.25205420
ANO_13.77-3.955.31505560
ANO_13.61-3.775.306190
ANO_13.47-3.615.17106330
ANO_13.34-3.474.84506510
ANO_13.23-3.344.82206800
ANO_13.13-3.234.72406860
ANO_13.04-3.134.47207630
ANO_12.95-3.044.43907310
ANO_12.87-2.954.13807880
ANO_12.8-2.873.97907750
ISO_211.91-37.621.2120.5117841
ISO_28.64-11.911.451.11517153
ISO_27.12-8.641.7441.07624861
ISO_26.19-7.121.6980.89831666
ISO_25.55-6.191.7151.03236476
ISO_25.08-5.551.6281.24840375
ISO_24.71-5.081.4940.83944065
ISO_24.41-4.711.4740.86848371
ISO_24.16-4.411.431.02250174
ISO_23.95-4.161.4310.89253966
ISO_23.77-3.951.4050.87155572
ISO_23.61-3.771.490.83861569
ISO_23.47-3.611.360.9163181
ISO_23.34-3.471.310.69865166
ISO_23.23-3.341.3460.88668080
ISO_23.13-3.231.3060.79868674
ISO_23.04-3.131.2480.75576375
ISO_22.95-3.041.2610.84973178
ISO_22.87-2.951.1870.6578971
ISO_22.8-2.871.180.82377273
ANO_211.91-37.622.0980690
ANO_28.64-11.915.30401670
ANO_27.12-8.645.80802450
ANO_26.19-7.125.45703140
ANO_25.55-6.194.86403610
ANO_25.08-5.554.24804020
ANO_24.71-5.083.25404360
ANO_24.41-4.713.65704780
ANO_24.16-4.413.7304990
ANO_23.95-4.163.46305350
ANO_23.77-3.953.33805550
ANO_23.61-3.773.33406150
ANO_23.47-3.613.17506310
ANO_23.34-3.472.85106490
ANO_23.23-3.342.97206790
ANO_23.13-3.232.83206860
ANO_23.04-3.132.55407630
ANO_22.95-3.042.56307310
ANO_22.87-2.952.407890
ANO_22.8-2.872.33107610
ISO_311.91-37.622.3970.977334
ISO_38.64-11.912.7651.67719259
ISO_37.12-8.642.9821.75225965
ISO_36.19-7.122.9751.54231966
ISO_35.55-6.193.0942.0636777
ISO_35.08-5.552.9572.28440475
ISO_34.71-5.082.7031.6544568
ISO_34.41-4.712.6361.33649175
ISO_34.16-4.412.4591.57351676
ISO_33.95-4.162.4511.44554271
ISO_33.77-3.952.381.55255674
ISO_33.61-3.772.4381.34261970
ISO_33.47-3.612.2341.43263381
ISO_33.34-3.472.130.46465167
ISO_33.23-3.342.0871.37568080
ISO_33.13-3.231.9951.02268674
ISO_33.04-3.131.8410.98476374
ISO_32.95-3.041.8441.19573178
ISO_32.87-2.951.6610.91378971
ISO_32.8-2.871.681.06177472
ANO_311.91-37.622.0310750
ANO_38.64-11.912.2802030
ANO_37.12-8.643.04202620
ANO_36.19-7.122.8503190
ANO_35.55-6.192.6203660
ANO_35.08-5.552.28604040
ANO_34.71-5.082.12304470
ANO_34.41-4.711.95204910
ANO_34.16-4.411.85905160
ANO_33.95-4.161.94605420
ANO_33.77-3.951.72305560
ANO_33.61-3.771.76506190
ANO_33.47-3.611.6406330
ANO_33.34-3.471.51906510
ANO_33.23-3.341.52506800
ANO_33.13-3.231.29306850
ANO_33.04-3.131.19207620
ANO_32.95-3.041.12407300
ANO_32.87-2.951.13207890
ANO_32.8-2.871.12407700
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å14.8 Å
Translation2.5 Å14.8 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
SHARPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→37.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.738 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2670 9.9 %RANDOM
Rwork0.196 ---
all0.197 26857 --
obs0.201 26857 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.352 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20 Å20 Å2
2--0.06 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2701 0 30 204 2935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222795
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.9743812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3695344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7324.574129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.44315443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8051518
X-RAY DIFFRACTIONr_chiral_restr0.1170.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022140
X-RAY DIFFRACTIONr_nbd_refined0.240.21350
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21896
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2189
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.215
X-RAY DIFFRACTIONr_mcbond_it1.191.51770
X-RAY DIFFRACTIONr_mcangle_it1.98522769
X-RAY DIFFRACTIONr_scbond_it2.74131197
X-RAY DIFFRACTIONr_scangle_it4.3424.51043
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 208 -
Rwork0.172 1704 -
obs-1912 100 %

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