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- PDB-3hav: Structure of the streptomycin-ATP-APH(2")-IIa ternary complex -

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Basic information

Entry
Database: PDB / ID: 3hav
TitleStructure of the streptomycin-ATP-APH(2")-IIa ternary complex
ComponentsAminoglycoside phosphotransferase
KeywordsTRANSFERASE / aminoglycoside / streptomycin / 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
ADENOSINE-5'-TRIPHOSPHATE / STREPTOMYCIN / Aminoglycoside phosphotransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.45 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 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Sep 6, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Aminoglycoside phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,53412
Polymers106,1953
Non-polymers3,3399
Water3,639202
1
A: Aminoglycoside phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5114
Polymers35,3981
Non-polymers1,1133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Aminoglycoside phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5114
Polymers35,3981
Non-polymers1,1133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Aminoglycoside phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5114
Polymers35,3981
Non-polymers1,1133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.620, 128.620, 57.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Aminoglycoside phosphotransferase


Mass: 35398.238 Da / Num. of mol.: 3
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-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A / Streptomycin


Mass: 581.574 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H39N7O12 / Comment: medication, antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 52.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 30% mPEG5000, 0.2 M MOPS/KOH pH 7.3, VAPOR DIFFUSION, HANGING 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: Jul 25, 2005
RadiationMonochromator: LN cooled, double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.45→42.9 Å / Num. obs: 41774 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 3ham

3ham


Resolution: 2.45→19.78 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 19.776 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28382 1943 5 %RANDOM
Rwork0.21756 ---
obs0.22075 37057 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.756 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20.96 Å20 Å2
2--1.91 Å20 Å2
3----2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7284 0 216 202 7702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227480
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.98910134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0085879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85824.935387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.733151282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1061536
X-RAY DIFFRACTIONr_chiral_restr0.0960.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025649
X-RAY DIFFRACTIONr_nbd_refined0.2330.23753
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25157
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2382
X-RAY DIFFRACTIONr_metal_ion_refined0.2530.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.294
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.220
X-RAY DIFFRACTIONr_mcbond_it0.4651.54488
X-RAY DIFFRACTIONr_mcangle_it0.80627022
X-RAY DIFFRACTIONr_scbond_it1.33333363
X-RAY DIFFRACTIONr_scangle_it2.0094.53110
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 141 -
Rwork0.29 2734 -
obs--98.26 %
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)
15.7155-0.65270.48042.24620.24.32930.0203-0.01120.2226-0.0303-0.01690.0588-0.6203-0.2663-0.0035-0.2640.040.0078-0.34970.0005-0.3215-6.9845.7052.006
25.0695-1.47630.17579.77870.34013.83290.03770.6815-0.1548-0.92490.1460.91380.0642-0.785-0.1838-0.3115-0.1538-0.15020.02880.1029-0.0045-26.142-3.131-8.545
33.4324-3.7162.74446.3713-3.70526.80930.31550.73670.2615-0.57330.254-0.1171-1.20270.0937-0.56950.23160.07260.05420.48850.0810.2447-29.2419.205-19.397
46.36040.16471.12873.9068-0.53194.15530.0840.04130.490.0426-0.1474-0.2073-0.52920.13190.0634-0.0618-0.04490.0121-0.2260.015-0.3727-56.58541.699-3.925
55.39980.5511.70858.1694-2.05484.7698-0.1906-0.6632-0.20310.4421-0.0735-0.65610.06670.54910.2641-0.14310.15470.00350.02860.0603-0.0635-38.74730.5026.581
63.35510.88191.51293.59021.31284.3222-0.1115-1.10461.06890.96270.2358-0.2757-0.94520.2416-0.12430.5291-0.1738-0.17720.7703-0.13030.6235-32.50251.98617.085
74.2371.39820.62613.61020.75415.9725-0.09980.1270.28010.1425-0.0029-0.064-0.7910.05780.1026-0.2711-0.0503-0.0255-0.35060.0355-0.329-59.256-29.727-6.183
85.1168-0.2351.17157.7079-1.42395.02650.1551-0.3699-0.54280.5156-0.2321-0.7313-0.08311.17980.077-0.3085-0.1775-0.22510.21820.1190.0587-37.75-34.0523.31
93.2651.6539-2.05711.8686-5.618121.6107-0.3852-0.95380.50650.9911-0.5517-0.1377-1.8496-0.49980.93691.1397-0.2267-0.21710.3627-0.08830.386-40.174-13.44216.412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 88
2X-RAY DIFFRACTION2A89 - 130
3X-RAY DIFFRACTION2A184 - 250
4X-RAY DIFFRACTION3A131 - 183
5X-RAY DIFFRACTION3A251 - 299
6X-RAY DIFFRACTION4B1 - 88
7X-RAY DIFFRACTION5B89 - 130
8X-RAY DIFFRACTION5B184 - 250
9X-RAY DIFFRACTION6B131 - 183
10X-RAY DIFFRACTION6B251 - 299
11X-RAY DIFFRACTION7C1 - 88
12X-RAY DIFFRACTION8C89 - 130
13X-RAY DIFFRACTION8C184 - 250
14X-RAY DIFFRACTION9C131 - 183
15X-RAY DIFFRACTION9C251 - 299

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