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- PDB-3q2j: Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type... -

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Basic information

Entry
Database: PDB / ID: 3q2j
TitleCrystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa Protein Kinase Inhibitor CKI-7 Complex
ComponentsAminoglycoside 3'-phosphotransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Ser/Thr/Tyr protein kinase / kinase / phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


kanamycin kinase / kanamycin kinase activity / response to antibiotic / ATP 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 ...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
Chem-CKI / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1501 Å
AuthorsFong, D.H. / Xiong, B. / Hwang, J. / Berghuis, A.M.
CitationJournal: Plos One / Year: 2011
Title: Crystal structures of two aminoglycoside kinases bound with a eukaryotic protein kinase inhibitor.
Authors: Fong, D.H. / Xiong, B. / Hwang, J. / Berghuis, A.M.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 17, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,6766
Polymers62,0242
Non-polymers6524
Water5,062281
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-38 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.837, 91.852, 131.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminoglycoside 3'-phosphotransferase / APH(3')III / Kanamycin kinase / type III / Neomycin-kanamycin phosphotransferase type III


Mass: 31012.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A3Y5, kanamycin kinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CKI / N-(2-AMINOETHYL)-5-CHLOROISOQUINOLINE-8-SULFONAMIDE


Mass: 285.750 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12ClN3O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 3000, Tris pH o8.0, 0.2M calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2003 / Details: mirrors
RadiationMonochromator: Si (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 33611 / Num. obs: 32199 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.07 / Net I/σ(I): 14.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 2567 / Rsym value: 0.24 / % possible all: 75.1

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J7L

1j7l


Resolution: 2.1501→46.587 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 3018 9.62 %random
Rwork0.1893 ---
all0.1937 33556 --
obs0.1937 31372 93.49 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.651 Å2 / ksol: 0.391 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.4193 Å2-0 Å20 Å2
2---1.4744 Å2-0 Å2
3---1.0551 Å2
Refinement stepCycle: LAST / Resolution: 2.1501→46.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 38 281 4645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084462
X-RAY DIFFRACTIONf_angle_d1.0816022
X-RAY DIFFRACTIONf_dihedral_angle_d14.2691710
X-RAY DIFFRACTIONf_chiral_restr0.075628
X-RAY DIFFRACTIONf_plane_restr0.004776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.2270.27052250.21732079X-RAY DIFFRACTION70
2.227-2.31610.26292720.20852414X-RAY DIFFRACTION82
2.3161-2.42150.2812880.20712748X-RAY DIFFRACTION91
2.4215-2.54920.26082510.21212934X-RAY DIFFRACTION96
2.5492-2.70890.27623540.21232892X-RAY DIFFRACTION98
2.7089-2.9180.26293540.20282941X-RAY DIFFRACTION98
2.918-3.21160.24423110.19192996X-RAY DIFFRACTION99
3.2116-3.67620.22523160.17983044X-RAY DIFFRACTION100
3.6762-4.63090.18713300.15583080X-RAY DIFFRACTION100
4.6309-46.59770.22713170.19573226X-RAY DIFFRACTION99

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