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- PDB-3ham: Structure of the gentamicin-APH(2")-IIa complex -

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Basic information

Entry
Database: PDB / ID: 3ham
TitleStructure of the gentamicin-APH(2")-IIa complex
ComponentsAminoglycoside phosphotransferase
KeywordsTRANSFERASE / aminoglycoside / gentamicin / antibiotic resistance
Function / homology
Function and homology information


transferase activity / ATP 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
Chem-LLL / Aminoglycoside phosphotransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsYoung, P.G. / Baker, E.N. / Vakulenko, S.B. / Smith, C.A.
CitationJournal: J.Bacteriol. / Year: 2009
Title: The crystal structures of substrate and nucleotide complexes of Enterococcus faecium aminoglycoside-2''-phosphotransferase-IIa [APH(2'')-IIa] provide insights into substrate selectivity in the APH(2'') subfamily.
Authors: Young, P.G. / Walanj, R. / Lakshmi, V. / Byrnes, L.J. / Metcalf, P. / Baker, E.N. / Vakulenko, S.B. / Smith, C.A.
History
DepositionMay 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 phosphotransferase
B: Aminoglycoside phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0648
Polymers70,7962
Non-polymers1,2676
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.700, 58.800, 81.400
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aminoglycoside phosphotransferase


Mass: 35398.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: aph(2')-Ib / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EVD7
#2: Chemical ChemComp-LLL / (2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL / GENTAMICIN C1A


Mass: 449.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H39N5O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: unbuffered 16% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2004
RadiationMonochromator: Si(111) double crystal, LN cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→80.6 Å / Num. obs: 25799 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 21.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→35 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.917 / SU B: 25.75 / SU ML: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.681 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27103 1299 5 %RANDOM
Rwork0.21002 ---
obs0.21319 24499 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.614 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20.29 Å2
2---3.12 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 86 238 5302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225158
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9826944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6945596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52925.072276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26615968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9191526
X-RAY DIFFRACTIONr_chiral_restr0.1040.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023834
X-RAY DIFFRACTIONr_nbd_refined0.2350.22565
X-RAY DIFFRACTIONr_nbtor_refined0.320.23532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2327
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.28
X-RAY DIFFRACTIONr_mcbond_it0.6021.53078
X-RAY DIFFRACTIONr_mcangle_it1.02424824
X-RAY DIFFRACTIONr_scbond_it1.65632343
X-RAY DIFFRACTIONr_scangle_it2.5174.52120
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 76 -
Rwork0.299 1688 -
obs--92.45 %
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)
14.82481.75232.20055.25670.62249.5704-0.0487-0.0458-0.2645-0.9814-0.0293-0.0170.7803-0.11780.078-0.1373-0.098-0.07860.3329-0.001-0.291-11.021-5.07911.88
24.1053-0.6779-0.56593.28780.69263.9927-0.0142-0.77680.0996-0.0196-0.0973-0.0332-0.0057-0.48840.1115-0.47060.0008-0.03590.407-0.0196-0.4198-0.7847.25928.879
34.57220.3117-0.43272.67251.76925.84170.1845-0.173-1.0611-0.1397-0.2236-0.6910.5151-0.08060.0391-0.33720.06930.00520.29570.15020.069219.421-2.39520.144
42.93870.1129-2.86283.9496-0.14928.050.1312-0.05350.0664-0.15240.0532-0.787-0.1013-0.0109-0.1844-0.016-0.09440.03840.45160.09150.121550.96330.56710.744
56.3112-0.5259-0.30635.7686-0.41573.44790.17-0.9337-0.60520.1017-0.1738-0.8414-0.29130.63660.0038-0.4724-0.0836-0.16010.52810.1805-0.267240.39119.22528.292
64.6244-0.37530.44763.8687-0.29056.80150.22790.03270.4413-0.4324-0.36120.2367-0.77310.16670.1333-0.25440.0676-0.10740.3001-0.0195-0.310620.15128.3718.96
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 88
2X-RAY DIFFRACTION2A89 - 129
3X-RAY DIFFRACTION2A184 - 250
4X-RAY DIFFRACTION3A130 - 183
5X-RAY DIFFRACTION3A251 - 299
6X-RAY DIFFRACTION4B1 - 88
7X-RAY DIFFRACTION5B89 - 129
8X-RAY DIFFRACTION5B184 - 250
9X-RAY DIFFRACTION6B130 - 183
10X-RAY DIFFRACTION6B251 - 299

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