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

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Basic information

Entry
Database: PDB / ID: 4fev
TitleCrystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor pyrazolopyrimidine PP1
ComponentsAminoglycoside 3'-phosphotransferase AphA1-IAB
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / pyrazolopyrimidine / PP1 / protein kinase inhibitor / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / ALPHA/BETA PROTEIN / TRANSFERASE / PHOSPHOTRANSFERASE / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / ANTIBIOTIC RESISTANCE / AMINOGLYCOSIDES / KANAMYCIN / GTP / INTRACELLULAR / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 phosphotransferase / Phosphotransferase enzyme family / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / 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
ACETATE ION / KANAMYCIN A / Chem-PP1 / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsStogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Minasov, G. / Egorova, O. / Di Leo, R. / Shakya, T. / Spanogiannopoulos, P. / Wright, G.D. / Savchenko, A. ...Stogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Minasov, G. / Egorova, O. / Di Leo, R. / Shakya, T. / Spanogiannopoulos, P. / 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
DepositionMay 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 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
Revision 1.4Sep 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

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
D: Aminoglycoside 3'-phosphotransferase AphA1-IAB
E: Aminoglycoside 3'-phosphotransferase AphA1-IAB
F: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,94826
Polymers186,1336
Non-polymers4,81520
Water25,2931404
1
A: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8114
Polymers31,0221
Non-polymers7893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8114
Polymers31,0221
Non-polymers7893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7883
Polymers31,0221
Non-polymers7662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8936
Polymers31,0221
Non-polymers8715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8114
Polymers31,0221
Non-polymers7893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8345
Polymers31,0221
Non-polymers8124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Aminoglycoside 3'-phosphotransferase AphA1-IAB
B: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6228
Polymers62,0442
Non-polymers1,5786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-33 kcal/mol
Surface area24020 Å2
MethodPISA
8
C: Aminoglycoside 3'-phosphotransferase AphA1-IAB
D: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6819
Polymers62,0442
Non-polymers1,6377
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-35 kcal/mol
Surface area23910 Å2
MethodPISA
9
E: Aminoglycoside 3'-phosphotransferase AphA1-IAB
F: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6459
Polymers62,0442
Non-polymers1,6017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-39 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.571, 94.217, 96.878
Angle α, β, γ (deg.)61.12, 73.09, 87.44
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 31022.139 Da / Num. of mol.: 6
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

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Non-polymers , 5 types, 1424 molecules

#2: Chemical
ChemComp-KAN / KANAMYCIN A


Mass: 484.499 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#3: Chemical
ChemComp-PP1 / 1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE


Mass: 281.356 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H19N5
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1404 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate, 18% PEG3350, 2% DMSO, 2 mM kanamycin, 3 mM PP1, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2010 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.89→20 Å / Num. obs: 132466 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.1 % / Rsym value: 0.047 / Net I/σ(I): 27.48
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.024 / Rsym value: 0.337 / % possible all: 96.5

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.phaser)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EJ7

4ej7


Resolution: 1.89→19.969 Å / SU ML: 0.21 / σ(F): 0.13 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2042 1972 1.54 %
Rwork0.1536 --
obs0.1543 128187 94.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-20.3554 Å2-0.9489 Å21.2442 Å2
2--8.7214 Å21.974 Å2
3---9.3457 Å2
Refinement stepCycle: LAST / Resolution: 1.89→19.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12576 0 335 1404 14315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713509
X-RAY DIFFRACTIONf_angle_d1.13118454
X-RAY DIFFRACTIONf_dihedral_angle_d12.4695002
X-RAY DIFFRACTIONf_chiral_restr0.0741993
X-RAY DIFFRACTIONf_plane_restr0.0052373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8901-1.95760.27131740.203311335X-RAY DIFFRACTION85
1.9576-2.03590.26031780.182411995X-RAY DIFFRACTION90
2.0359-2.12850.21621860.164512275X-RAY DIFFRACTION92
2.1285-2.24060.24471970.158612521X-RAY DIFFRACTION94
2.2406-2.38070.18672080.156812720X-RAY DIFFRACTION95
2.3807-2.56420.24191970.163512857X-RAY DIFFRACTION96
2.5642-2.82160.22512030.172512975X-RAY DIFFRACTION97
2.8216-3.22840.23192020.166813188X-RAY DIFFRACTION98
3.2284-4.06190.17432100.139213162X-RAY DIFFRACTION99
4.0619-19.97030.17562170.133613187X-RAY DIFFRACTION99
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)
11.78620.2350.19131.40470.2142.0970.1539-0.1918-0.1582-0.25280.13340.9092-0.2739-0.48830.0745-0.35080.1033-0.00120.19680.13720.3946-25.8255-18.0717-13.6363
21.0425-0.3302-0.2031.27380.37041.7564-0.0193-0.0134-0.08640.0205-0.00150.09570.13450.06230.00340.0253-0.00110.0040.03750.02310.0721-3.0402-28.6259-17.4229
32.40310.3810.51511.4890.20742.6326-0.0043-0.22730.21830.1780.08120.6697-0.4864-0.44890.08090.22560.10140.1030.19090.04170.3412-24.5973-4.8449-6.4321
40.7283-0.1542-0.00252.7855-0.25941.26750.0147-0.07850.10850.32640.0648-0.0526-0.4071-0.0052-0.05930.2622-0.01160.04750.0786-0.01590.1492-2.74828.5328-8.4576
51.0994-0.475-0.52822.7288-0.19972.17560.00080.03970.03570.02850.02610.3449-0.1649-0.2233-0.01780.1155-0.0493-0.03170.063-0.02590.1362-5.5723-59.2644-29.7471
60.9638-0.1266-0.25581.0531-0.23091.4241-0.041-0.13710.0310.2079-0.0385-0.11030.00630.1710.00260.1341-0.0144-0.07820.0724-0.03140.063515.8254-58.2686-19.7455
72.0417-0.2035-0.88092.0749-0.37031.91160.05020.3884-0.0454-0.3271-0.14340.29060.0496-0.36040.05650.15440.0143-0.08620.1696-0.0390.1645-4.2168-61.7994-46.6457
80.85070.02220.08871.21630.34552.0573-0.00410.0460.03710.05070.0141-0.14660.06760.1384-0.01130.03890.00550.01920.09250.00140.058519.3503-71.9503-55.2191
91.6227-0.40311.54012.2625-0.15222.52830.06310.0413-0.0454-0.3155-0.00160.2540.097-0.1112-0.03860.1068-0.00410.00150.14270.01890.084611.5645-53.387310.7874
101.41320.3088-0.03961.718-0.37241.64690.00520.20340.1295-0.31850.04020.02150.19640.0689-0.0340.12490.03210.00610.1270.0175-0.005534.1538-47.07577.2855
112.6551-1.2547-0.25843.12630.2412.17850.0883-0.4822-0.68910.57630.27970.65870.648-0.9071-0.12290.3478-0.2004-0.01850.47690.23930.131312.0749-69.975826.53
120.7429-0.023-0.20851.8656-0.47211.58050.0296-0.0149-0.016-0.0817-0.0221-0.1151-0.01360.0792-0.01130.0401-0.01190.00580.07410.01370.051135.0204-71.387236.5773
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
7X-RAY DIFFRACTION7chain D and resid 1:102
8X-RAY DIFFRACTION8chain D and resid 103:271
9X-RAY DIFFRACTION9chain E and resid 1:102
10X-RAY DIFFRACTION10chain E and resid 103:271
11X-RAY DIFFRACTION11chain F and resid 1:102
12X-RAY DIFFRACTION12chain F and resid 103:271

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