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- PDB-3n4u: app APH(2")-IVa form II -

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Basic information

Entry
Database: PDB / ID: 3n4u
Titleapp APH(2")-IVa form II
ComponentsAPH(2'')-Id
KeywordsUNKNOWN FUNCTION / aminoglycoside / phosphotransferase / resistance
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
: / 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
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSmith, C.A. / Toth, M. / Frase, H. / Vakulenko, S.B.
CitationJournal: Protein Sci. / Year: 2010
Title: Crystal structure and kinetic mechanism of aminoglycoside phosphotransferase-2''-IVa.
Authors: Toth, M. / Frase, H. / Antunes, N.T. / Smith, C.A. / Vakulenko, S.B.
History
DepositionMay 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APH(2'')-Id


Theoretical massNumber of molelcules
Total (without water)35,4251
Polymers35,4251
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.380, 62.590, 96.490
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 APH(2'')-Id


Mass: 35425.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / References: UniProt: O68183
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 1.98 Å3/Da / Density % sol: 37.77 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→28.61 Å / Num. all: 16313 / Num. obs: 16313 / % possible obs: 96 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.8
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.3 / % possible all: 81

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→28.61 Å / SU ML: 0.32 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2728 727 5 %
Rwork0.1784 --
obs0.183 14542 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.727 Å2 / ksol: 0.282 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.8221 Å2-0 Å2-0 Å2
2---5.7671 Å2-0 Å2
3----3.055 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2495 0 0 232 2727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082588
X-RAY DIFFRACTIONf_angle_d1.0423496
X-RAY DIFFRACTIONf_dihedral_angle_d17.905978
X-RAY DIFFRACTIONf_chiral_restr0.073369
X-RAY DIFFRACTIONf_plane_restr0.004451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.36970.31931380.21472629X-RAY DIFFRACTION96
2.3697-2.60770.31861460.20142776X-RAY DIFFRACTION99
2.6077-2.98390.28391460.18832764X-RAY DIFFRACTION100
2.9839-3.75520.25061470.15642803X-RAY DIFFRACTION99
3.7552-19.82550.24511500.16062843X-RAY DIFFRACTION97

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