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

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Basic information

Entry
Database: PDB / ID: 4feu
TitleCrystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor anthrapyrazolone SP600125
ComponentsAminoglycoside 3'-phosphotransferase AphA1-IAB
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / anthrapyrazolone / SP600125 / 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
2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE / ACETATE ION / KANAMYCIN A / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 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 1.1Mar 20, 2013Group: Other
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Aug 7, 2013Group: Database references
Revision 1.4Sep 4, 2013Group: Database references
Revision 1.5Sep 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 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)192,02421
Polymers188,1026
Non-polymers3,92215
Water12,160675
1
A: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1144
Polymers31,3501
Non-polymers7643
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)31,8943
Polymers31,3501
Non-polymers5442
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)32,1735
Polymers31,3501
Non-polymers8234
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)31,8943
Polymers31,3501
Non-polymers5442
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)32,0553
Polymers31,3501
Non-polymers7052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Aminoglycoside 3'-phosphotransferase AphA1-IAB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8943
Polymers31,3501
Non-polymers5442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.752, 94.161, 96.766
Angle α, β, γ (deg.)61.21, 73.11, 87.36
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 31350.404 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
#2: Chemical
ChemComp-KAN / KANAMYCIN A / Kanamycin A


Mass: 484.499 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#3: Chemical ChemComp-537 / 2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE / 1,9-Pyrazoloanthrone


Mass: 220.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H8N2O / Comment: inhibitor*YM
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M sodium acetate pH 4.5, 8% PEG3350, 3% DMSO, 0.2 M NDSB221, 2 mM kanamycin, 3 mM SP600125, 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: 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: 2.37→20 Å / Num. obs: 67481 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 2.7 % / Biso Wilson estimate: 50.58 Å2 / Rsym value: 0.072 / Net I/σ(I): 16.35
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2 / Rsym value: 0.423 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.phaser)model building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 4EJ7

4ej7


Resolution: 2.37→19.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.9257 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 3406 5.05 %RANDOM
Rwork0.1601 ---
obs0.1628 67481 --
Displacement parametersBiso mean: 55.88 Å2
Baniso -1Baniso -2Baniso -3
1--8.3895 Å21.5914 Å22.905 Å2
2--5.3945 Å2-2.6674 Å2
3---2.995 Å2
Refine analyzeLuzzati coordinate error obs: 0.279 Å
Refinement stepCycle: LAST / Resolution: 2.37→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12320 0 273 675 13268
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112987HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0717662HARMONIC2
X-RAY DIFFRACTIONt_trig_c_planes359HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1835HARMONIC5
X-RAY DIFFRACTIONt_it12717HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.8
X-RAY DIFFRACTIONt_other_torsion18.48
X-RAY DIFFRACTIONt_chiral_improper_torsion1567SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact14859SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 218 4.59 %
Rwork0.1882 4534 -
all0.1896 4752 -
obs-4752 -
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)
12.49730.33011.76912.5839-0.43232.92130.2367-0.1514-0.0047-0.3331-0.04950.50940.1588-0.4214-0.1872-0.09970.0263-0.0005-0.0154-0.0035-0.0343-25.042822.4375-12.3724
21.9194-0.24060.28172.788-1.05821.71290.17820.4103-0.011-0.4707-0.15640.10840.25420.2177-0.0219-0.03960.07860.0190.0436-0.0293-0.2372-2.834128.3799-17.4759
31.5722-1.18270.81082.68780.01081.22420.0404-0.569-0.31010.1180.25010.30810.4568-0.3656-0.2905-0.103-0.1147-0.02280.01060.1171-0.0991-25.25968.3381-1.5237
40.90020.43460.06362.3091-0.78511.67760.07320.0277-0.1729-0.1231-0.0575-0.22520.1220.1779-0.0157-0.05650.037-0.0052-0.0744-0.0064-0.0504-2.08633.956111.6729
53.28951.2876-0.35851.5903-1.14363.07140.1342-0.338-0.4371-0.25720.15990.38990.2204-0.568-0.2942-0.1993-0.0203-0.0348-0.03710.20970.1041-62.318552.8516-39.01
62.0906-0.47950.35121.27480.65362.04350.121-0.0525-0.3037-0.0065-0.00210.17820.20610.0841-0.1189-0.0617-0.014-0.007-0.10190.0873-0.0398-39.72646.8971-42.0484
72.24280.0514-0.71520.11080.05390.11050.0127-0.39120.40270.08370.09350.3917-0.3993-0.0267-0.1061-0.03960.09120.2057-0.01340.08370.0574-60.914674.6295-30.5912
81.9075-0.22340.31793.8566-0.62672.5374-0.1603-0.42790.44990.38470.1175-0.0172-0.4349-0.16060.0428-0.00890.02040.0605-0.2195-0.0817-0.1132-39.651284.0471-33.2551
91.95520.09830.05711.9543-0.53251.55540.0548-0.06740.2246-0.1556-0.0070.6493-0.0102-0.2213-0.0478-0.0735-0.0141-0.1266-0.1548-0.03930.1149-43.148917.3756-54.1205
101.62240.0996-0.4071.0684-0.23941.657-0.0717-0.19920.16660.1056-0.0250.0378-0.02470.12090.0967-0.00950.0385-0.1249-0.108-0.0637-0.0161-21.123817.2973-44.4936
113.0774-1.59730.1167-0.60890.15542.96530.07540.39370.1103-0.42-0.20860.18720.3666-0.30330.13320.1064-0.0057-0.2373-0.11-0.0289-0.056-40.167511.7213-75.7186
121.5849-0.03170.73971.49020.19292.8721-0.19740.30690.26160.13030.0152-0.2395-0.1970.3570.1821-0.0815-0.0267-0.0027-0.0410.0643-0.1102-17.66563.5084-79.8461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|19 - A|102 }A19 - 102
2X-RAY DIFFRACTION2{ A|103 - A|271 }A103 - 271
3X-RAY DIFFRACTION3{ B|2 - B|102 }B2 - 102
4X-RAY DIFFRACTION4{ B|103 - B|271 }B103 - 271
5X-RAY DIFFRACTION5{ C|5 - C|102 }C5 - 102
6X-RAY DIFFRACTION6{ C|103 - C|271 }C103 - 271
7X-RAY DIFFRACTION7{ D|25 - D|102 }D25 - 102
8X-RAY DIFFRACTION8{ D|103 - D|271 }D103 - 271
9X-RAY DIFFRACTION9{ E|6 - E|102 }E6 - 102
10X-RAY DIFFRACTION10{ E|103 - E|271 }E103 - 271
11X-RAY DIFFRACTION11{ F|21 - F|102 }F21 - 102
12X-RAY DIFFRACTION12{ F|103 - F|271 }F103 - 271

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