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

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Basic information

Entry
Database: PDB / ID: 4fex
TitleCrystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor tyrphostin AG1478
ComponentsAminoglycoside 3'-phosphotransferase AphA1-IAB
Keywordstransferase/transferase INHIBITOR / tyrphostin / 4-anilinoquinazoline / tyrphostin AG1478 / AG1478 / 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
Chem-0TO / ACETATE ION / KANAMYCIN A / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,90117
Polymers155,1115
Non-polymers3,79112
Water3,135174
1
A: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8454
Polymers31,0221
Non-polymers8233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5303
Polymers31,0221
Non-polymers5072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8814
Polymers31,0221
Non-polymers8593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8223
Polymers31,0221
Non-polymers8002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8223
Polymers31,0221
Non-polymers8002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.669, 93.694, 96.318
Angle α, β, γ (deg.)118.84, 103.56, 93.44
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 5 molecules ABCDE

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


Mass: 31022.139 Da / Num. of mol.: 5 / 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 , 5 types, 186 molecules

#2: Chemical
ChemComp-KAN / KANAMYCIN A


Mass: 484.499 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#3: Chemical
ChemComp-0TO / N-(3-chlorophenyl)-6,7-dimethoxyquinazolin-4-amine


Mass: 315.754 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14ClN3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / 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.: 174 / 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: 2.8 Å3/Da / Density % sol: 56.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 2.5
Details: 0.1 M sodium acetate pH 4.5, 14% PEG3350, 0.3 M NDSB221, 2% DMSO, 2 mM kanamycin, 5 mM tyrphostin AG1478, 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: Feb 18, 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: 2.71→20 Å / Num. obs: 45480 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.9 % / Rsym value: 0.061 / Net I/σ(I): 19.39
Reflection shellResolution: 2.71→2.76 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.043 / Num. unique all: 2305 / Rsym value: 0.562 / % possible all: 98.5

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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: 2.71→19.901 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1939 4.48 %random
Rwork0.184 ---
obs0.1866 45056 97.86 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.46 Å2 / ksol: 0.302 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.3024 Å20.7903 Å2-2.3843 Å2
2--12.9744 Å21.8103 Å2
3----6.268 Å2
Refinement stepCycle: LAST / Resolution: 2.71→19.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10328 0 259 174 10761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110976
X-RAY DIFFRACTIONf_angle_d1.30414953
X-RAY DIFFRACTIONf_dihedral_angle_d15.174067
X-RAY DIFFRACTIONf_chiral_restr0.081622
X-RAY DIFFRACTIONf_plane_restr0.0051928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.80660.3783980.30398496X-RAY DIFFRACTION98
2.8066-2.91870.34073940.26918544X-RAY DIFFRACTION98
2.9187-3.0510.32823980.23298514X-RAY DIFFRACTION98
3.051-3.21130.344010.21738595X-RAY DIFFRACTION98
3.2113-3.41150.27244000.19798453X-RAY DIFFRACTION98
3.4115-3.67340.23434020.18728514X-RAY DIFFRACTION98
3.6734-4.04030.21424040.16658568X-RAY DIFFRACTION98
4.0403-4.61850.24090.14778521X-RAY DIFFRACTION98
4.6185-5.7950.23353840.16228571X-RAY DIFFRACTION98
5.795-19.90140.19374040.16968431X-RAY DIFFRACTION97

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