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- PDB-3sg9: Crystal Structure of Aminoglycoside-2''-Phosphotransferase Type I... -

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Basic information

Entry
Database: PDB / ID: 3sg9
TitleCrystal Structure of Aminoglycoside-2''-Phosphotransferase Type IVa Kanamycin A Complex
ComponentsAPH(2'')-Id
KeywordsTRANSFERASE/ANTIBIOTIC / Antibiotic resistance enzyme / Transferase / Aminoglycoside / Phosphotransferase / TRANSFERASE-ANTIBIOTIC complex
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
KANAMYCIN A / APH(2'')-Id
Similarity search - Component
Biological speciesEnterococcus casseliflavus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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)72,5445
Polymers71,5392
Non-polymers1,0043
Water3,153175
1
A: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2542
Polymers35,7701
Non-polymers4841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: APH(2'')-Id
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2903
Polymers35,7701
Non-polymers5202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-11 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.903, 101.426, 73.399
Angle α, β, γ (deg.)90.00, 100.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35769.605 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-KAN / KANAMYCIN A


Mass: 484.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H36N4O11 / Comment: antibiotic*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 16, 2011 / Details: VariMax HF
RadiationMonochromator: Confocal dual reflection mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. all: 32419 / Num. obs: 32322 / % possible obs: 99.7 % / Redundancy: 7 % / Rsym value: 0.32
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 3356 / Rsym value: 0.32 / % possible all: 98.9

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.04 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25052 1685 5 %RANDOM
Rwork0.19537 ---
all0.19829 31904 --
obs0.19829 31811 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.421 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å2-0.03 Å2
2---2 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 67 175 5074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225042
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9826831
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32125.159252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75115884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1631517
X-RAY DIFFRACTIONr_chiral_restr0.1240.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213809
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.061.52981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8824838
X-RAY DIFFRACTIONr_scbond_it3.13432061
X-RAY DIFFRACTIONr_scangle_it4.7814.51988
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 109 -
Rwork0.19 2321 -
obs--98.94 %
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)
10.38740.009-0.05511.1673-0.25120.2271-0.036-0.0271-0.01520.0980.03450.1165-0.0230.00510.00150.06680.00230.02980.00650.00540.02299.974218.767531.8795
20.4057-0.1271-0.12961.16350.06750.06660.00060.0218-0.002-0.0951-0.0017-0.0644-0.0036-0.04370.00110.05590.0046-0.02890.0748-0.00730.028616.12934.90261.7652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 297
2X-RAY DIFFRACTION2B1 - 297

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