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- PDB-3tdw: The GDP complex of the aminoglycoside 2'-phosphotransfere-IIIa F1... -

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Basic information

Entry
Database: PDB / ID: 3tdw
TitleThe GDP complex of the aminoglycoside 2'-phosphotransfere-IIIa F108L mutant
ComponentsGentamicin resistance protein
KeywordsTRANSFERASE / kinase / phosphoryl transfer / antibiotic resistance
Function / homology
Function and homology information


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
GUANOSINE-5'-DIPHOSPHATE / Gentamicin resistance protein
Similarity search - Component
Biological speciesEnterococcus gallinarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Aminoglycoside 2''-Phosphotransferase IIIa (APH(2'')-IIIa) Prefers GTP over ATP: STRUCTURAL TEMPLATES FOR NUCLEOTIDE RECOGNITION IN THE BACTERIAL AMINOGLYCOSIDE-2'' KINASES.
Authors: Smith, C.A. / Toth, M. / Frase, H. / Byrnes, L.J. / Vakulenko, S.B.
History
DepositionAug 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2012Group: Database references
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Gentamicin resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2356
Polymers34,6941
Non-polymers5405
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.060, 54.690, 77.810
Angle α, β, γ (deg.)90.00, 108.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Gentamicin resistance protein


Mass: 34694.215 Da / Num. of mol.: 1 / Mutation: F108L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus gallinarum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P96762
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.25 M MgCl2, 0.1 M Tris HCl, 20% (w/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: RAYONIX MX-325 / Detector: CCD / Date: Nov 23, 2007
RadiationMonochromator: Si(222) liquid nitrogen cooled double crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→46 Å / Num. all: 36432 / Num. obs: 36432 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.8
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 1.7→19.21 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1821 5 %random 5%
Rwork0.1738 ---
obs0.1762 36427 99.74 %-
all-36427 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.739 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.7453 Å20 Å25.015 Å2
2---3.5162 Å2-0 Å2
3----4.2291 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 32 403 2845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072569
X-RAY DIFFRACTIONf_angle_d1.1393489
X-RAY DIFFRACTIONf_dihedral_angle_d18.432964
X-RAY DIFFRACTIONf_chiral_restr0.071386
X-RAY DIFFRACTIONf_plane_restr0.005453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7460.3081200.26352648X-RAY DIFFRACTION100
1.746-1.79730.30011410.24032647X-RAY DIFFRACTION100
1.7973-1.85530.25971450.20782636X-RAY DIFFRACTION100
1.8553-1.92150.23621250.20082680X-RAY DIFFRACTION100
1.9215-1.99840.28341230.19112671X-RAY DIFFRACTION100
1.9984-2.08920.23861530.1842633X-RAY DIFFRACTION100
2.0892-2.19920.19641370.17342647X-RAY DIFFRACTION100
2.1992-2.33680.23661410.16542643X-RAY DIFFRACTION100
2.3368-2.51680.19591570.17542669X-RAY DIFFRACTION100
2.5168-2.76940.22571170.17942699X-RAY DIFFRACTION100
2.7694-3.16860.25511480.17922647X-RAY DIFFRACTION100
3.1686-3.98630.17891590.14872663X-RAY DIFFRACTION100
3.9863-19.2110.1831550.14482723X-RAY DIFFRACTION99

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