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- PDB-3n4t: apo APH(2")-IVa form I -

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Basic information

Entry
Database: PDB / ID: 3n4t
Titleapo APH(2")-IVa form I
ComponentsAPH(2'')-Id
KeywordsUNKNOWN FUNCTION / aminoglycoside / phosphotransferase / resistance
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
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
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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 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
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.060, 63.610, 101.340
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.: 136 / 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: 2.28 Å3/Da / Density % sol: 45.99 %

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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→29.8 Å / Num. all: 16673 / Num. obs: 16673 / % possible obs: 97.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.2

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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→29.8 Å / SU ML: 0.32 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2429 834 5 %
Rwork0.187 --
obs0.1899 16670 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.156 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.9073 Å2-0 Å2-0 Å2
2---5.5461 Å2-0 Å2
3----3.3612 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 0 136 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072520
X-RAY DIFFRACTIONf_angle_d1.0113396
X-RAY DIFFRACTIONf_dihedral_angle_d18.216944
X-RAY DIFFRACTIONf_chiral_restr0.07358
X-RAY DIFFRACTIONf_plane_restr0.005439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.33780.33911350.2392575X-RAY DIFFRACTION98
2.3378-2.51830.32271390.21122640X-RAY DIFFRACTION99
2.5183-2.77150.29521390.20692636X-RAY DIFFRACTION99
2.7715-3.17220.28851400.19832655X-RAY DIFFRACTION99
3.1722-3.99510.22021390.16882649X-RAY DIFFRACTION98
3.9951-29.83690.18851420.15552681X-RAY DIFFRACTION94
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)
11.2520.8577-0.66780.772-0.21121.4727-0.0614-0.127-0.0234-0.23870.0388-0.0310.40950.1908-00.25210.07280.02660.21920.00890.16356.09446.3703-37.0126
20.330.33820.06591.08560.59261.2814-0.10330.02020.1126-0.18520.15210.11550.1237-0.0316-0.00010.132-0.038-0.05010.23210.05450.343-13.90585.7664-26.15
30.4530.10540.40880.78860.16830.3471-0.0179-0.0352-0.05830.33780.0814-0.10380.02540.052-00.40150.0545-0.06210.2955-0.00480.26143.33271.1574-1.934
40.86340.23650.2511.4097-0.24921.6341-0.070.06390.19120.08860.09980.1395-0.05530.021200.15950.00140.01910.22960.02090.2877-12.77287.7176-22.652
50.9482-0.24250.56010.2377-0.13250.3305-0.1939-0.11620.18550.28950.0891-0.073-0.3201-0.012200.46230.0317-0.0220.28040.00280.32751.117310.3221-8.6641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:99
2X-RAY DIFFRACTION2chain A and resid 100:145
3X-RAY DIFFRACTION3chain A and resid 146:189
4X-RAY DIFFRACTION4chain A and resid 190:255
5X-RAY DIFFRACTION5chain A and resid 256:297

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