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- PDB-3sg8: Crystal Structure of Aminoglycoside-2''-Phosphotransferase Type I... -

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Basic information

Entry
Database: PDB / ID: 3sg8
TitleCrystal Structure of Aminoglycoside-2''-Phosphotransferase Type IVa Tobramycin Complex
ComponentsAPH(2'')-Id
KeywordsTRANSFERASE/ANTIBIOTIC / Antibiotic resistance enzyme / Transferase / Aminoglycoside / Phosphorylation / TRANSFERASE-ANTIBIOTIC complex
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
TOBRAMYCIN / APH(2'')-Id
Similarity search - Component
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsShi, K. / Houston, D.R. / Berghuis, A.M.
CitationJournal: Biochemistry / Year: 2011
Title: Crystal Structures of Antibiotic-Bound Complexes of Aminoglycoside 2''-Phosphotransferase IVa Highlight the Diversity in Substrate Binding Modes among Aminoglycoside Kinases.
Authors: Shi, K. / Houston, D.R. / Berghuis, A.M.
History
DepositionJun 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: APH(2'')-Id
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6876
Polymers71,6812
Non-polymers1,0064
Water6,125340
1
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3443
Polymers35,8411
Non-polymers5032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3443
Polymers35,8411
Non-polymers5032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-30 kcal/mol
Surface area28490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.334, 101.479, 73.455
Angle α, β, γ (deg.)90.00, 100.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein APH(2'')-Id


Mass: 35840.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus casseliflavus (bacteria) / Gene: aph(2'')-Id / Production host: Escherichia coli (E. coli) / References: UniProt: O68183
#2: Chemical ChemComp-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL


Mass: 467.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37N5O9 / Comment: antibiotic*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM HEPES, 17% PEG4000, 10% glycerol, 5% isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 25, 2011
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. all: 57787 / Num. obs: 57440 / % possible obs: 99.4 % / Redundancy: 5.1 % / Rsym value: 0.059
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 5717 / Rsym value: 0.349 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→33.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.41 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24208 2900 5.1 %RANDOM
Rwork0.18544 ---
all0.18828 54791 --
obs0.18828 54440 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.24 Å2
2---0.25 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4857 0 66 340 5263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225114
X-RAY DIFFRACTIONr_angle_refined_deg1.8891.986938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49425.097257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82615903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3721518
X-RAY DIFFRACTIONr_chiral_restr0.1410.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213878
X-RAY DIFFRACTIONr_mcbond_it1.1931.53015
X-RAY DIFFRACTIONr_mcangle_it2.01424903
X-RAY DIFFRACTIONr_scbond_it3.35432099
X-RAY DIFFRACTIONr_scangle_it5.0764.52022
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 187 -
Rwork0.222 4018 -
obs--99.67 %
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)
16.3874-0.685-2.7148.68141.42823.559-0.05580.3250.1048-0.80110.09571.13070.3046-0.3171-0.040.1929-0.0899-0.1350.14330.04140.163-18.9078.519-23.782
21.0883-0.58590.49971.7798-0.5411.01170.0298-0.0105-0.0238-0.1604-0.0320.21240.19040.08260.00220.1608-0.01420.04810.12070.01630.0854-8.58911.557-15.412
30.9477-0.42730.29031.6749-0.61841.46-0.0063-0.1048-0.0446-0.0268-0.0077-0.1650.00560.01020.0140.10140.01920.05860.12890.01770.0760.9758.6531.612
41.0718-0.4379-0.30682.82520.38330.29770.0021-0.02670.03350.08640.0199-0.4059-0.0382-0.0484-0.02190.161-0.04650.05030.117-0.00280.1397-0.63339.7830.185
51.14820.67330.17413.0548-0.1560.6620.00310.01520.0444-0.01680.04350.0316-0.0056-0.0681-0.04670.11690.00990.05610.13140.02050.0751-1.69511.581-1.805
62.4262-0.32050.14562.9203-0.62811.2365-0.0655-0.22850.19710.27570.0492-0.1628-0.1075-0.08080.01630.16350.01870.00840.1385-0.00410.05341.12415.4988.578
71.7469-1.70660.95164.2493-1.55290.8509-0.0751-0.010.00870.33660.19140.246-0.0985-0.0396-0.11630.1382-0.01060.07080.11240.01180.1124-6.87930.2223.053
83.24210.09620.80032.24730.74171.59780.0343-0.17380.01690.0437-0.05440.1784-0.0628-0.13220.02010.08650.00670.03090.1886-0.00870.0783-16.56246.936-20.531
91.5947-0.0736-0.32640.90040.03330.5140.07430.0192-0.01620.0126-0.0044-0.02010.00990.0559-0.06990.09390.0031-0.00160.1764-0.01220.0676-4.67242.656-24.933
100.7468-0.36680.41842.5032-0.61872.1890.00020.0389-0.0093-0.1876-0.0482-0.3046-0.0798-0.08320.04790.0752-0.02190.06460.1794-0.00480.073410.56843.822-37.766
112.77811.3110.18432.55730.84340.68560.07990.0171-0.18390.0676-0.0014-0.3433-0.0664-0.0438-0.07850.1078-0.0194-0.02790.1376-0.00050.11784.41713.261-38.14
120.7398-0.27370.07613.4339-0.3040.8404-0.01050.2429-0.1364-0.1029-0.0213-0.0917-0.0226-0.15360.03180.0748-0.01520.03720.1966-0.03080.08746.32641.583-35.693
133.8510.43890.60033.0288-0.12312.12890.10180.4084-0.4375-0.5259-0.1045-0.42420.1426-0.04920.00280.173-0.00330.11430.2209-0.07850.14611.98337.178-44.394
143.47912.15780.30963.33250.65120.1867-0.2010.2207-0.0476-0.40220.2332-0.1213-0.09930.0365-0.03220.19570.02450.0240.1516-0.00780.01410.68623.165-42.541
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 97
3X-RAY DIFFRACTION3A98 - 144
4X-RAY DIFFRACTION4A145 - 189
5X-RAY DIFFRACTION5A190 - 225
6X-RAY DIFFRACTION6A226 - 253
7X-RAY DIFFRACTION7A254 - 298
8X-RAY DIFFRACTION8B1 - 23
9X-RAY DIFFRACTION9B24 - 97
10X-RAY DIFFRACTION10B98 - 144
11X-RAY DIFFRACTION11B145 - 189
12X-RAY DIFFRACTION12B190 - 225
13X-RAY DIFFRACTION13B226 - 253
14X-RAY DIFFRACTION14B254 - 298

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