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- PDB-2b0q: Crystal Structure Of 3',5"-Aminoglycoside Phosphotransferase Type... -

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Basic information

Entry
Database: PDB / ID: 2b0q
TitleCrystal Structure Of 3',5"-Aminoglycoside Phosphotransferase Type IIIa ADP Neomycin B Complex
ComponentsAminoglycoside 3'-phosphotransferase
KeywordsTRANSFERASE / protein kinase-like
Function / homology
Function and homology information


kanamycin kinase / kanamycin kinase activity / phosphorylation / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / NEOMYCIN / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsFong, D.H. / Berghuis, A.M.
CitationJournal: Embo J. / Year: 2002
Title: Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry.
Authors: Fong, D.H. / Berghuis, A.M.
History
DepositionSep 14, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionSep 27, 2005ID: 1L8U
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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_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.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_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_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_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9715
Polymers30,8811
Non-polymers1,0904
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.357, 46.357, 301.613
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Aminoglycoside 3'-phosphotransferase / Kanamycin kinase / type III / Neomycin-kanamycin phosphotransferase / type III / APH3' / III


Mass: 30880.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: aphA / Plasmid: pETSACG1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A3Y5, kanamycin kinase
#2: Chemical ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN


Mass: 614.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H46N6O13 / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.6 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 600, CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2000
RadiationMonochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. all: 9987 / Num. obs: 8074 / % possible obs: 80.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 11.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4.3 / Num. unique all: 457 / Rsym value: 0.168

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1L8T

1l8t


Resolution: 2.7→46.36 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.312 852 8.6 %random
Rwork0.225 ---
all0.225 9927 --
obs0.225 8027 80.9 %-
Solvent computationBsol: 54.011 Å2
Displacement parametersBiso mean: 42.929 Å2
Baniso -1Baniso -2Baniso -3
1-1.611 Å20 Å20 Å2
2--1.611 Å20 Å2
3----3.221 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.76 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.7→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 71 45 2286
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007855
X-RAY DIFFRACTIONc_angle_deg1.39623
X-RAY DIFFRACTIONc_dihedral_angle_d21.93355
X-RAY DIFFRACTIONc_improper_angle_d0.83803
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.05
RfactorNum. reflection% reflection
Rfree0.462 87 -
Rwork0.298 --
obs-713 50.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2atp.par
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4nmy.par
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.param

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