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- PDB-1j7u: Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type... -

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Basic information

Entry
Database: PDB / ID: 1j7u
TitleCrystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa AMPPNP Complex
ComponentsAMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
KeywordsTRANSFERASE / antibiotic resistance / kinase / ATP-binding
Function / homology
Function and homology information


kanamycin kinase / kanamycin kinase activity / response to antibiotic / ATP 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 ...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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Aminoglycoside 3'-phosphotransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsBurk, D.L. / Hon, W.C. / Leung, A.K.-W. / Berghuis, A.M.
Citation
Journal: Biochemistry / Year: 2001
Title: Structural analyses of nucleotide binding to an aminoglycoside phosphotransferase.
Authors: Burk, D.L. / Hon, W.C. / Leung, A.K. / Berghuis, A.M.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Structure of an Enzyme Required for Antibiotic Resistance Reveals Homology to Eukaryotic Protein Kinases
Authors: Hon, W.C. / McKay, G.A. / Thompson, P.R. / Sweet, R.M. / Yang, D.S.C. / Wright, G.D. / Berghuis, A.M.
History
DepositionMay 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

Downloads & links

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Assembly

Deposited unit
A: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
B: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1348
Polymers62,0242
Non-polymers1,1106
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-59 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.168, 91.321, 132.653
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


Mass: 31012.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pPCRG6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A3Y5, kanamycin kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, isopropanol, HEPES, magnesium chloride, AMPPNP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
21 mMmagnesium sulfate1drop
35 mMHEPES1drop
410 mM1dropMgCl2
5100 mMHEPES1reservoir
620 %(w/v)PEG40001reservoir
710 %(v/v)2-propanol1reservoir

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Data collection

DiffractionMean temperature: 106 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→39.8 Å / Num. all: 24507 / Num. obs: 24507 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 19.5
Reflection shellResolution: 2.4→2.55 Å / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 3 / % possible all: 97.9
Reflection
*PLUS
Num. obs: 92600 / Num. measured all: 24507
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→39.8 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 41525417 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2358 9.9 %RANDOM
Rwork0.217 ---
obs-23845 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.17 Å2 / ksol: 0.3174 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---2.26 Å20 Å2
3---2.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.4→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 66 188 4594
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it2.832
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 381 10.3 %
Rwork0.248 3325 -
obs--92.6 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.251
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.12
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.309 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.248

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