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

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Basic information

Entry
Database: PDB / ID: 4few
TitleCrystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor pyrazolopyrimidine PP2
ComponentsAminoglycoside 3'-phosphotransferase AphA1-IAB
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / pyrazolopyrimidine / PP2 / 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 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
ACETATE ION / KANAMYCIN A / DI(HYDROXYETHYL)ETHER / Chem-PP2 / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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_alt_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_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)193,58934
Polymers188,1026
Non-polymers5,48728
Water21,0781170
1
A: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2556
Polymers31,3501
Non-polymers9055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2205
Polymers31,3501
Non-polymers8694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2444
Polymers31,3501
Non-polymers8933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3027
Polymers31,3501
Non-polymers9516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2205
Polymers31,3501
Non-polymers8694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3497
Polymers31,3501
Non-polymers9986
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)64,47511
Polymers62,7012
Non-polymers1,7749
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-65 kcal/mol
Surface area23990 Å2
MethodPISA
8
C: Aminoglycoside 3'-phosphotransferase AphA1-IAB
D: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,54611
Polymers62,7012
Non-polymers1,8459
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-36 kcal/mol
Surface area23520 Å2
MethodPISA
9
E: Aminoglycoside 3'-phosphotransferase AphA1-IAB
F: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,56912
Polymers62,7012
Non-polymers1,86810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-59 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.280, 93.579, 96.399
Angle α, β, γ (deg.)61.22, 73.18, 87.35
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: 31350.404 Da / Num. of mol.: 6 / Fragment: APHA1-IAB
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 , 7 types, 1198 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-PP2 / 1-TERT-BUTYL-3-(4-CHLORO-PHENYL)-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE


Mass: 302.782 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H17ClN5
#4: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1170 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate, 14% PEG3350, 3% DMSO, 2 mM kanamycin, 3 mM PP2, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2011 / 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: 1.97→23.899 Å / Num. obs: 115884 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.1 % / Rsym value: 0.068 / Net I/σ(I): 19.26
Reflection shellResolution: 1.97→2 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.146 / Rsym value: 0.405 / % possible all: 96.7

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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: 1.98→23.899 Å / SU ML: 0.22 / σ(F): 0.09 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 5461 4.93 %
Rwork0.1569 --
obs0.1598 111054 92.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.983 Å2-1.5001 Å21.8192 Å2
2---1.5059 Å23.4485 Å2
3----2.4771 Å2
Refinement stepCycle: LAST / Resolution: 1.98→23.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12580 0 370 1170 14120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913509
X-RAY DIFFRACTIONf_angle_d1.14318432
X-RAY DIFFRACTIONf_dihedral_angle_d12.6914999
X-RAY DIFFRACTIONf_chiral_restr0.0731983
X-RAY DIFFRACTIONf_plane_restr0.0052374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00250.34042960.2515811X-RAY DIFFRACTION80
2.0025-2.0260.29013130.22866016X-RAY DIFFRACTION82
2.026-2.05070.27033240.22436144X-RAY DIFFRACTION83
2.0507-2.07670.29713090.21246237X-RAY DIFFRACTION85
2.0767-2.1040.2953210.21076335X-RAY DIFFRACTION85
2.104-2.13280.25052880.19816332X-RAY DIFFRACTION86
2.1328-2.16320.2613410.1916444X-RAY DIFFRACTION87
2.1632-2.19550.28583530.18796566X-RAY DIFFRACTION88
2.1955-2.22980.24813320.17886444X-RAY DIFFRACTION89
2.2298-2.26630.24533450.18266584X-RAY DIFFRACTION90
2.2663-2.30540.26953620.1836771X-RAY DIFFRACTION91
2.3054-2.34730.26943530.17536661X-RAY DIFFRACTION91
2.3473-2.39240.24053570.16936780X-RAY DIFFRACTION92
2.3924-2.44110.22213290.15926758X-RAY DIFFRACTION92
2.4411-2.49420.21753880.15996971X-RAY DIFFRACTION94
2.4942-2.55210.21163320.16726877X-RAY DIFFRACTION94
2.5521-2.61590.25213660.15727009X-RAY DIFFRACTION94
2.6159-2.68650.2163690.166937X-RAY DIFFRACTION95
2.6865-2.76550.21843720.16617009X-RAY DIFFRACTION95
2.7655-2.85460.25383590.16487115X-RAY DIFFRACTION96
2.8546-2.95640.24183810.16326990X-RAY DIFFRACTION97
2.9564-3.07460.22863650.16587120X-RAY DIFFRACTION97
3.0746-3.21420.23783810.16737290X-RAY DIFFRACTION97
3.2142-3.38320.21663600.15417121X-RAY DIFFRACTION98
3.3832-3.59450.20883810.14957295X-RAY DIFFRACTION98
3.5945-3.8710.18133680.12587219X-RAY DIFFRACTION98
3.871-4.25850.1793770.12147201X-RAY DIFFRACTION98
4.2585-4.87020.15253680.11677308X-RAY DIFFRACTION99
4.8702-6.11890.19723830.14787206X-RAY DIFFRACTION99
6.1189-23.90110.16973850.157180X-RAY DIFFRACTION97
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)
12.12110.15660.53371.71610.49772.76110.0896-0.3415-0.2627-0.05720.02520.7332-0.0747-0.6163-0.06450.17560.0214-0.01970.32390.10150.4641-25.9764-18.1255-12.7393
21.363-0.4107-0.1251.31720.53922.3931-0.0093-0.0506-0.1431-0.01280.0310.13020.22590.1119-0.02440.1447-0.00170.00380.13760.04950.1704-2.8732-29.3258-16.3079
32.89110.25020.86862.06860.84354.2604-0.0465-0.4256-0.00640.19860.03510.7302-0.447-0.77430.09350.27910.11070.1220.37690.10110.4381-24.9004-5.3134-4.9915
41.1743-0.084-0.09514.5986-0.53631.9460.0041-0.16730.23360.2240.1618-0.0071-0.47510.0796-0.15470.2966-0.03240.03780.1985-0.03080.2218-2.61517.7141-7.7336
51.5491-1.4085-0.7143.3887-1.1724.5345-0.01270.0633-0.00550.05860.08150.3603-0.1181-0.4527-0.06580.205-0.0535-0.04190.1631-0.04180.2683-5.2593-60.031-29.1836
61.19880.165-0.3021.5118-0.56272.343-0.0537-0.14170.02020.2933-0.0362-0.1445-0.03720.24120.08060.24120.0042-0.06410.1459-0.02220.178315.7737-58.8-18.9386
72.459-0.2254-1.69512.4019-0.5433.58210.01980.4417-0.1191-0.278-0.10310.28260.1868-0.50960.09110.2350.0051-0.08430.2188-0.02410.2786-3.5616-62.45-46.0318
81.1608-0.14290.21551.44530.42182.7711-0.04820.09770.07520.0536-0.0047-0.17960.030.23040.05870.12210.00570.01590.1780.0250.159819.3488-72.3819-54.0778
92.6047-0.09772.81063.3244-0.62073.3190.123-0.0979-0.1025-0.25320.06920.38170.1749-0.175-0.18620.17410.01080.04820.22750.04270.169711.7299-53.966513.3434
101.28990.1519-0.10243.0622-0.95671.9780.03830.25850.0172-0.5152-0.0217-0.02150.260.1666-0.02780.26310.0220.00970.26370.01020.116934.038-47.79997.9955
112.1267-1.14321.37733.37370.41562.11290.0255-0.4326-0.41770.44130.140.46530.3486-0.4703-0.14540.3019-0.07710.02190.31240.07280.253612.4025-67.442123.4408
121.13170.16-0.07042.8994-0.64311.7730.06550.0045-0.0652-0.046-0.078-0.14920.01020.11590.0050.12110.00650.00310.15230.01560.13534.6039-71.519837.4829
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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