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- PDB-4ej7: Crystal structure of the aminoglycoside phosphotransferase APH(3'... -

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Basic information

Entry
Database: PDB / ID: 4ej7
TitleCrystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, ATP-bound
ComponentsAminoglycoside 3'-phosphotransferase AphA1-IAB
KeywordsTRANSFERASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / ALPHA/BETA PROTEIN / PHOSPHOTRANSFERASE / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / ANTIBIOTIC RESISTANCE / AMINOGLYCOSIDES / KANAMYCIN / GTP / INTRACELLULAR
Function / homology
Function and homology information


kanamycin kinase / kanamycin kinase activity / phosphorylation / response to antibiotic / ATP binding / metal ion binding
Similarity search - Function
Aminoglycoside 3-phosphotransferase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsStogios, P.J. / Minasov, G. / Tan, K. / Evdokimova, E. / Egorova, O. / Di Leo, R. / Shakya, T. / Wright, G.D. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Biochem.J. / Year: 2013
Title: Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance.
Authors: Stogios, P.J. / Spanogiannopoulos, P. / Evdokimova, E. / Egorova, O. / Shakya, T. / Todorovic, N. / Capretta, A. / Wright, G.D. / Savchenko, A.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionApr 18, 2012ID: 3R78
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Sep 4, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminoglycoside 3'-phosphotransferase AphA1-IAB
B: Aminoglycoside 3'-phosphotransferase AphA1-IAB
C: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,42419
Polymers101,3153
Non-polymers2,10916
Water5,296294
1
A: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5457
Polymers33,7721
Non-polymers7746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4797
Polymers33,7721
Non-polymers7086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3995
Polymers33,7721
Non-polymers6274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules

A: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,09114
Polymers67,5442
Non-polymers1,54712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area8320 Å2
ΔGint-114 kcal/mol
Surface area24740 Å2
MethodPISA
5
B: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules

B: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,95914
Polymers67,5442
Non-polymers1,41512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7440 Å2
ΔGint-119 kcal/mol
Surface area24330 Å2
MethodPISA
6
C: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules

C: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,79810
Polymers67,5442
Non-polymers1,2558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7730 Å2
ΔGint-109 kcal/mol
Surface area24780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.363, 152.466, 165.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-555-

HOH

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Components

#1: Protein Aminoglycoside 3'-phosphotransferase AphA1-IAB


Mass: 33771.828 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AYE / Gene: ABAYE3578, APHA1-IAB / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0VD92, kanamycin kinase
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M CA ACETATE, 16% PEG3350, 2 MM ATP, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.29→43.669 Å / Num. obs: 91198 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Net I/σ(I): 12.552
Reflection shellResolution: 2.29→2.3 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.5298 / % possible all: 69.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.29→43.669 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2516 3790 4.19 %random
Rwork0.2134 ---
obs0.215 90409 96.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.351 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.8067 Å2-0 Å20 Å2
2--31.4101 Å2-0 Å2
3---20.1465 Å2
Refinement stepCycle: LAST / Resolution: 2.29→43.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6472 0 112 294 6878
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096879
X-RAY DIFFRACTIONf_angle_d0.6949395
X-RAY DIFFRACTIONf_dihedral_angle_d12.752535
X-RAY DIFFRACTIONf_chiral_restr0.043980
X-RAY DIFFRACTIONf_plane_restr0.0031215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2903-2.37220.34483590.32058391X-RAY DIFFRACTION93
2.3722-2.46720.32913830.29558699X-RAY DIFFRACTION97
2.4672-2.57940.37293810.29278801X-RAY DIFFRACTION97
2.5794-2.71540.33433820.26628735X-RAY DIFFRACTION97
2.7154-2.88550.31033880.25198662X-RAY DIFFRACTION97
2.8855-3.10820.29853830.25028756X-RAY DIFFRACTION97
3.1082-3.42090.31343910.22328656X-RAY DIFFRACTION97
3.4209-3.91570.22443750.2018768X-RAY DIFFRACTION97
3.9157-4.93230.21313790.16348650X-RAY DIFFRACTION96
4.9323-43.67650.19333690.19618501X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.14260.02360.07040.0644-0.01140.11880.0930.0342-0.4693-0.1860.1506-0.034-0.065-0.08950.2115-0.14480.187-0.240.07490.1560.174284.109325.000947.5867
20.1336-0.110.00460.13380.04150.1559-0.028-0.08-0.0447-0.01710.0761-0.03-0.0155-0.1490.00390.2077-0.00660.02290.1811-0.00160.151273.994447.678456.6634
30.1989-0.00590.1670.1977-0.04430.48350.37110.1106-0.18-0.150.21060.31770.1586-0.05720.30980.20630.0024-0.08660.21450.17750.384933.132173.40175.7129
40.0862-0.1129-0.08350.07380.0820.09710.06680.0498-0.00660.0435-0.07370.11610.12170.0347-0.00060.27740.0263-0.01330.1835-0.01270.172256.007664.403467.8521
50.0509-0.02490.01560.0803-0.0260.17340.18060.04080.1764-0.0386-0.06860.00030.1725-0.04590.01520.16740.00390.00630.2642-0.0170.221944.069829.778147.9276
60.12410.03770.04830.12160.03240.12980.1276-0.2442-0.41240.0038-0.0391-0.05350.00940.09970.08340.2703-0.0692-0.15130.31430.06730.276454.11117.014856.7389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:102
2X-RAY DIFFRACTION2chain A and resid 103:271
3X-RAY DIFFRACTION3chain B and resid 1:102
4X-RAY DIFFRACTION4chain B and resid 103:271
5X-RAY DIFFRACTION5chain C and resid 1:102
6X-RAY DIFFRACTION6chain C and resid 103:271

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